Pilarcitos Integrated Watershed Management Plan: Pilarcitos Creek Restoration Workgroup

December 31, 2007
Pilarcitos Integrated Watershed

Management Plan
Prepared for
Pilarcitos Creek Restoration Workgroup
1910
2007
Prepared by
Philip Williams & Associates, Ltd.

with Sound Watershed Consulting, H.T. Harvey & Associates,
D.W. Alley & Associates, Jerry Smith, PhD, and Weber-Hayes & Associates
Pilarcitos PRELIMINARY DRAFT Integrated Watershed Management Plan
Prepared for
San Mateo Resource Conservation District
Prepared by
with
Sound Watershed Consulting
H.T. Harvey & Associates
D.W. Alley & Associates
Jerry Smith, PhD
Weber-Hayes & Associates
December 31, 2007
PWA REF. # 1884 T4

Services provided pursuant to this Agreement are intended solely for the
use and benefit of the San Mateo Resource Conservation District.
No other person or entity shall be entitled to rely on the services,

opinions, recommendations, plans or specifications provided pursuant
to this agreement without the express written consent of Philip
Williams & Associates, Ltd., 550 Kearny Street, Suite 900, San
Francisco, CA 94108.
P:\Projects\1884_Pilarcitos_IWMP\Task4_IWMP\reports\Draft Pilarcitos IWMP\Preliminary Draft Pilarcitos IWMP.doc
12/28/07
TABLE OF CONTENTS
Page No.
1. EXECUTIVE SUMMARY 1
2. INTRODUCTION AND PLANNING APPROACH 3
3. PLAN GOALS & OBJECTIVES 5
4. KEY WATERSHED MANAGEMENT ISSUES 8
4.1
INSTREAM FLOWS 8
4.1.1 Instream Flow Improvement Opportunities 8
4.1.2 Water Supply Infrastructure 9
4.1.3 Grey Water Sources & Uses 9
4.2 ECOSYSTEM FUNCTIONS & PROCESSES 9
4.2.1 Fish Passage & Instream Habitat 10
4.2.2 Watershed Erosion and Sedimentation 10
4.2.3 Channel Maintenance 10
4.2.4 Riparian Vegetation and Habit 11
4.2.5 Control of Exotic and Invasive Vegetation 11
4.2.6 Lagoon Habitat 11
4.3 WATERSHED MANAGEMENT ISSUES 11
4.3.1 Community Engagement 11
4.3.2 Beach Quality 12
4.3.3 Landowner Concerns 12
4.3.4 Landfill Issues 12
5. PRELIMINARY PROPOSED PROJECTS 13
5.1 PROJECT EVALUATION PROCESS 13

5.1.1 Criteria for Project Priorities 14
5.2 IMPROVEMENT PROJECT SUMMARIES 18
5.2.1 Arroyo Leon Ponds Rehabilitation 18
5.2.2 Stone Dam Flow Releases 19
5.2.3 Remedial Action on the Lower Arroyo Leon Fish Passage Project 19
5.2.4 Remedial Action on the Mills Creek Fish Passage Project at the
Historical Bridge 20
5.2.5 Modification of Barrier 1 on Lower Apanolio Creek 20
5.2.6 Modification of Bongard’s Pond Operation and the Channel
Downstream 21
5.2.7 Modification of the 2007 Fish Passage Project at Barrier 3 on Apanolio
Creek 22
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5.2.8
Apanolio Flashboard Dam and Apron Removal, Downstream of the
BFI Property Line 22
5.2.9 Lower Pilarcitos Streamflow Improvements 23
5.2.10 Erosion Control Projects 23
5.2.11 Stream Maintenance & Restoration Support 24
5.2.12 Fish Habitat Enhancement Opportunities 24
5.2.13 Other Enhancement Activities (template) 25
5.3 FEASIBILITY STUDIES 25
5.3.1 Lagoon Restoration Feasibility Study 25
5.3.2 Pilarcitos Lake Dead Storage Access Feasibility Study 26
5.3.3 Grey Water Utilization Study 26
5.3.4 Riparian Conservation Easement Program Feasibility Study 27
5.4 PLANNING PROJECT SUMMARIES 28
5.4.1 Eucalyptus Control Planning 28
5.4.2 Watershed Monitoring Program 28
5.5 ADDITIONAL ASSESSMENT PROJECT SUMMARIES 29
5.5.1 Water Budget Development Project(s) 29
5.5.2 Road Assessment Project 30
5.5.3 Geomorphic Channel Assessment 31
5.5.4 Arroyo Leon Fish Habitat Assessment 32
5.5.5 Fish Habitat Assessment 32
5.5.6 Riparian Habitat Restoration and Invasive Plant Eradication
Assessment 33
5.5.7 Assess Habitat Management and Restoration Opportunities for
Sensitive Wetland Species 35
5.5.8 Watershed-Scale Sensitive Plants and Habitats Assessment 35
6. IMPLEMENTATION STRATEGY 37
6.1
LEAD AGENCY RESPONSIBILITIES 37
6.2
FUNDING SOURCES 37
6.3
MILESTONES 37
6.4
MONITORING & ADAPTIVE MANAGEMENT 37
6.4.1 Implementation Monitoring 38
6.4.2 Effectiveness Monitoring 38
6.4.3 Validation Monitoring 38
6.4.4 Resource Objectives & Performance Measures 38
7. REFERENCES 39
8. LIST OF PREPARERS 40
9. FIGURES 41
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LIST OF APPENDICES
Appendix A. Watershed Assessment Update
Appendix B. Workgroup Memorandum of Understanding
LIST OF TABLES
Table 1. Example Project Criteria Matrix
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1. EXECUTIVE SUMMARY
The Pilarcitos watershed (Figure 1) is a significant area of great ecological, cultural and economic
diversity. It is a source of clean drinking water for residents of the central coast and San Francisco Bay
Area and supports several natural resource-based economies – including commercial fishing, agriculture
and recreational tourism. The watershed is also experiencing increased competition for water between
agricultural, domestic, recreational, commercial and environmental uses.
The purpose of the Pilarcitos Integrated Watershed Management Plan (IWMP) is to promote balanced
solutions to effectively manage the Pilarcitos Creek watershed that satisfy environmental, public health,
domestic water supply, and economic interests. It will achieve this purpose by prioritizing restoration
projects that individually or collectively help to achieve six key goals, described in Section 3 and
summarized here:
1. Protect and recover Steelhead trout and other native aquatic & riparian species
2. Enhance streamflows while maintaining yield
3. Manage stream channels corridors to reduce erosion, sedimentation and flood risks
4. Increase native riparian vegetation
5. Maintain good water quality conditions
6. Promote community and stakeholder collaboration
These goals were developed to address several key watershed management issues that were identified
following a review of information about the existing state of the watershed (Appendix A). The key
watershed management issues affecting the goals of the IWMP include the following:
• Instream flows to support aquatic resources during critical summer and fall periods.
• Other ecosystem factors, including fish passage, instream habitat, watershed erosion, channel
maintenance, riparian vegetation, exotic invasive species, and the summer lagoon.
• Social issues, including community engagement, landowner concerns, beach quality, and landfill
issues.
This Preliminary Draft IWMP identifies 12 improvement projects, 4 feasibility projects, 2 planning
projects and 8 additional assessment projects. We expect that stakeholders will modify and augment this
list with additional projects. Additional project details are also expected to be added based on input from
stakeholders.
In Section 5.1, we identify an objective project evaluation process that will integrate project priorities
using both scientific and management criteria. Project rankings will be determined through a facilitated
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process between the consulting team responsible for this report and stakeholders identified in the
Memorandum of Understanding (MOU) (Appendix B).
The key factors affecting the IWMP Implementation Strategy are outlined in Section 6. There we briefly
describe our initial thinking with respect to identifying lead agency responsibilities, funding sources,
IWMP milestones, and elements of an adaptive management strategy. Additional details for these sections
will be developed out of the results of the project priorities as well as additional discussions with the
stakeholder group.
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2. INTRODUCTION AND PLANNING APPROACH
The Pilarcitos watershed (Figure 1) is a significant area of great ecological, cultural and economic
diversity. While it is located near one of the most heavily populated areas of California, it remains
relatively undeveloped, and large portions of the watershed retain many of the natural features that existed
prior to human occupation. The Pilarcitos watershed is a source of clean drinking water for residents of
the central coast and San Francisco Bay Area. The Pilarcitos watershed also supports several natural
resource-based economies – including commercial fishing, agriculture and recreational tourism.
The Pilarcitos watershed is a significant environmental resource, rich in native plant and animal species.
Pilarcitos Creek originates on the eastern side of Montara Mountain and flows about 12 miles to the
Pacific Ocean near the City of Half Moon Bay in California. It is the principal watercourse draining a
coastal watershed of 17,922 acres in San Mateo County. The creek originates on land owned by the San
Francisco Public Utilities Commission, then passes through Coastside County Water District land;
private, residential, and agricultural lands; and lands owned by other public entities including the City of
Half Moon Bay, State Parks, and Sewer Authority Mid-Coastside before draining into the Pacific.
Pilarcitos Creek is also identified as critical habitat for the recovery of Steelhead trout, federally listed as
threatened.
The watershed will face several challenges in the next few decades. Housing demands in the San
Francisco Bay Area will likely cause increased development pressures in the watershed. Dams,
diversions, and indirect impacts from various land-use activities have combined to reduce fish and
wildlife habitat, degrade stream channels, block access to steelhead spawning, and increase exotic species
invasions. The watershed is also experiencing increased competition for water between agricultural,
domestic, recreational, commercial and environmental uses.
The purpose of the Pilarcitos Integrated Watershed Management Plan (IWMP) is to promote balanced
solutions to effectively manage the Pilarcitos Creek watershed that satisfy environmental, public health,
domestic water supply, and economic interests. The Pilarcitos IWMP will help to coordinate water
management efforts among a broad spectrum of community interests by identifying common projects,
aligning resources, and increasing collaboration among these interests. An important component of the
Pilarcitos IWMP is an assessment of existing conditions and a strategy for addressing the actions
necessary for the protection and restoration of steelhead and other species of concern that depend on
aquatic and riparian habitats throughout the watershed.
This Preliminary Draft IWMP was developed by a consultant team with the oversight of the Pilarcitos
Workgroup, consisting of representatives from over nineteen or more partnering entities, including local,
state and federal agencies and local community and advocacy groups. The Workgroup is guided by a
Memorandum of Understanding (MOU) (see Appendix B), and has developed input from all affected
stakeholders in the process, including local utilities, the agricultural community, public and private
landowners, state and federal regulatory agencies, advocacy groups, local residents, and elected officials.
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The success of any planning process hinges upon balancing the issues and concerns of the stakeholders.
The Pilarcitos watershed is a relatively small watershed with a diverse set of uses. Many of the building
blocks for achieving watershed improvements are in place, and there is broad agreement that additional
work can be beneficial.
However, there are many uncertainties about specific ecological processes and the effect of watershed
management practices on those processes. To date, incomplete scientific data and inconsistent monitoring
practices limit our knowledge of the cumulative effects of land-use practices on the desired functions and
conditions in the watershed. The Pilarcitos IWMP documents our understanding of the existing watershed
conditions, and identifies data gaps that currently exist.
Based on an analysis of the existing condition of the watershed, the consultant team and Workgroup
established a set of goals and objectives for the IWMP (Section 3). This document describes key
watershed management issues (Section 4) and recommends a set of projects that will help to achieve the
goals and objectives developed by the Workgroup (Section 5). The preliminary set of projects includes
specific improvement projects, feasibility studies, planning programs, and additional assessment projects
that will help close data gaps. We also include a process for evaluating and prioritizing key projects
(Section 5.1), and we briefly discuss some of the key implementation factors that will need to be
addressed before the final IWMP is completed (Section 6).
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3. PLAN GOALS & OBJECTIVES
The purpose of the Pilarcitos Integrated Watershed Management Plan is to promote balanced solutions to
effectively manage the Pilarcitos Creek watershed that satisfy environmental, public health, domestic
water supply, and economic interests. The Preliminary Draft IWMP establishes a set of goals that define
broad types of actions that will combine to achieve the purpose of the IWMP. For each goal a series of
objectives offers more specific guidance about how each goal will be achieved. The goals and objectives
reflect agreement by the Workgroup achieved through an ongoing dialogue. Together, the goals and
objectives provide a foundation for the Implementation Strategy and Plan.
Goal 1: Federally-listed Steelhead trout and other native species that depend on aquatic and
riparian environments are protected and recovered by providing habitat sufficient for
sustainable population levels while maintaining water supply yield for users.
Objective 1A: Where practical, remove or modify any significant (population- limiting)
barriers to steelhead access to fair or better spawning or rearing habitat.
Objective 1B: Provide an abundance of rearing habitats by supplementing existing rearing
habitat with additional restored and managed habitat features.
Objective 1C: Implement water conservation measures as well as active and passive
riparian habitat restoration programs to support a robust riparian corridor dominated by
locally-native riparian plant species.
Objective 1D: Increase existing summer and fall streamflow to Pilarcitos Creek and its
estuary to maintain sustainable populations of native species that depend on aquatic and
riparian environments.
Objective 1E: Provide guidelines for incorporating large wood in streams while balancing
benefits with streambank erosion and flooding hazards.
Objective 1F: Control non-native predators of California red-legged frog (i.e. bullfrogs) via
managing hydroperiods and implementing active predator eradication programs in
locations where this is feasible (i.e. off-channel ponds).
Goal 2: Cost-effective, stakeholder-supported alternative water supply and water recycling

projects are developed to enhance streamflows while maintaining yield for users.
Objective 2A: Manage flows to improve aquatic habitat and to improve conditions that
support native, riparian habitat (e.g., willow/alder-dominated riparian habitat, instream
wetlands).
Objective 2B: Improve efficiency and operations in existing water storage and delivery
systems.
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Objective 2C: Implement recycled water projects to reduce demand for Pilarcitos Creek
streamflows.
Objective 2D: Control the expansion and begin to reduce the extent of riparian eucalyptus
to reduce summer water loss.
Objective 2E: Implement Objective 1D: above.
Goal 3: Stream channels and their floodplains are restored or managed to resist erosion
and sedimentation and to minimize flood risks.
Objective 3A: Integrate ecologic value into channel treatment designs that accommodate
natural geomorphic processes.
Objective 3B: Implement best management practices to limit erosion along channels and on
hillslopes in the short and long-term, with vegetative cover or other surface erosion
control measures.
Objective 3C: Re-establish native riparian vegetation on bare streambanks to increase
stability and function and to improve the aesthetic and habitat quality of the riparian
corridor.
Objective 3D: Implement best management practices and projects to reduce total sediment
delivery from both human land use sources and natural background levels.
Goal 4: Native vegetation is increased with prioritized attention to special-status plant

species, and exotic and invasive plant species are managed and removed.
Objective 4A: Improve degraded habitat to increase the spatial extent, distribution, and
amount of native riparian forest, freshwater wetlands, and off-channel ponds/wetlands
and support native species populations and biodiversity.
Objective 4B: Remove invasive non-native plant species from the riparian corridors of the
watershed. See Objective 2E: above.
Objective 4C: Implement Objective 1D: above.
Goal 5: Activities to maintain good water quality conditions are implemented for both
human and biotic uses.
Objective 5A: Control or mitigate pollution at the source prior to delivery to the stream
network.
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Objective 5B: Maintain water quality at the highest practical level, exceeding all regulatory
standards.
Objective 5C: Develop monitoring program or acquire baseline and monitoring data
Objective 5D: Implement Objective 1A: above.
Objective 5E: Implement Objective 1A: above.
Objective 5F: Implement Objective 1D: above.
Goal 6: Extensive community and stakeholder collaboration in watershed management

occurs.
Objective 6A: Develop and make available essential data to inform watershed management
practices and decisions.
Objective 6B: Increase community awareness of watershed processes and habitat through
such means as newsletters and riparian and agricultural landowner outreach and
educational workshops.
Objective 6C: Provide informational resources for interested organizations and teachers and
a framework for student and volunteer engagement in watershed management activities.
Objective 6D: Develop a long-term monitoring and reporting program to evaluate the
success of the restoration projects and to adjust treatments based on the monitoring
results.
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4. KEY WATERSHED MANAGEMENT ISSUES
There are a number of watershed issues within the Pilarcitos watershed that frame the context for the
Integrated Watershed Management Plan. The following section outlines some of the more essential
issues, including strategies for addressing them, and provides a framework for collaboration with
stakeholders within the watershed. These issues summarize information that is discussed in considerable
detail in the Watershed Assessment Update (Appendix A).
4.1 INSTREAM FLOWS
One of the most important limiting factors for both fish habitat and water quality in the Pilarcitos is the
summer instream flows that have typically been low under recorded historical conditions. Low flows limit
fish migration, reduce available rearing habitat, and retain pollutants in the stream environment. Many of
the other opportunities for improvement in the Pilarcitos watershed hinge upon the ability to improve
summer and fall instream flows in the lower watershed.
Streamflow is affected by diversions, dams, domestic and irrigation wells, and stock ponds. It also is
influenced by water supply infrastructure management practices, land-use practices, allocation of water
rights, and the need to maintain important ecosystem functions and processes. The following sections
briefly describe some of these key issues.
4.1.1 Instream Flow Improvement Opportunities
Summertime instream flow conditions in Lower Pilarcitos (Figure 1) have been significantly lower than
other creeks along the central coast. Retention of water at Pilarcitos Lake and its diversions at Stone Dam
eliminated a significant portion of the contributing watershed area. Baseflow from tributary basins have
been insufficient to compensate for the lack of water from Upper Pilarcitos. Prior to 1997, it was not
uncommon for Pilarcitos Creek at Half Moon Bay to be dry for 30 or more days each year. After 1998, a
minimum flow level has been maintained throughout the year, although the volume of flow in summer
has remained low.
The 2007 summer flows in Lower Pilarcitos, as measured at Half Moon Bay by the USGS, generally have
exceeded the 80th percentile of historic summer flows for this station over its 40 years of record. This
trend occurred despite the otherwise dry conditions along most of the other coastal streams. The source of
this additional water can be traced back to releases below Stone Dam, which are 2-4 times higher in 2007
than they have been over the last 10 years (the period of record below Stone Dam). The improved 2007
flow conditions, as well as improved lagoon conditions, offer a perspective for opportunities to improve
instream flows.
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4.1.2 Water Supply Infrastructure
The existing water supply infrastructure depends in part on antiquated delivery systems that were
designed and constructed, in some cases, in the 19th Century. Water routinely is transferred out of the
basin, and stored in Crystal Springs Reservoir. Water must then be pumped back over the ridge to supply
the CCWD as needs require. Improvements to the water supply infrastructure could lead to more efficient
water use, reduced evaporative losses, and more overall control of water delivery for instream, domestic
and commercial uses. Specific efficiency estimates are not currently available given the lack of a record
of the volume of water deliveries from SFPUC to CCWD.
4.1.3 Grey Water Sources & Uses
Grey water describes non-industrial wastewater generated from domestic processes such as washing
dishes, laundry and bathing. It also can describe runoff from certain light industrial or agricultural uses
that do not introduce significant pollutants (e.g. heavy metals, toxins, fecal waste, etc). By contrast,
“black water” typically contains larger amounts of chemical and biological contaminants (from feces or
toxic chemicals). Grey water gets its name from its cloudy appearance.
Grey water resources provide an opportunity to improve the availability of water supply in areas like the
Pilarcitos where freshwater supplies exceed available demand. It can be particularly useful for
commercial irrigation, domestic sewage (e.g. toilet supplies), or industrial cooling applications. Such
treatments usually require modest treatments to address public health and aesthetic concerns.
Existing water use regulations in many jurisdictions preclude the use of grey water, often treating it as
sewage. Many of the regulations preventing the use of grey water are based on public health issues.
However, with water conservation becoming increasingly important in the Pilarcitos watershed, it may be
appropriate for the community to reconsider the actual risks against potential benefits. Recently, an
increasing number of regulatory jurisdictions are coming to accept that the microbiological risks of grey
water reuse at the individual domestic level can be insignificant, if well managed. Recent regulatory and
law changes in Montana, Germany and Australia offer some insight into approaches that can be used to
address risks while improving water supply.
4.2 ECOSYSTEM FUNCTIONS & PROCESSES
One of the primary requirements of Integrated Watershed Management Planning is the need to protect
key ecosystem functions and processes. Many of the natural functions within the watershed help to
support key watershed beneficial uses. For example, wetlands help to improve water quality. Stable
channels help to reduce flood losses to agricultural entities and streamside residents, as well as protect
capital infrastructure like roads, bridges, buildings, etc. By supporting these natural functions, the cost of
repairs and maintenance of the infrastructure can be reduced.
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There are also public resources that must be maintained for the benefit of the entire community.
Commercial fish stocks require a functional stream and estuary environment. The broader community
also places high aesthetic values on riparian areas, streamside corridors and public beaches. A clean water
supply is also a very important public need. All of these functions can be sustained with attention to these
key ecosystem processes.
4.2.1 Fish Passage & Instream Habitat
There is broad support for improving conditions for resident steelhead and native fish. Steelhead access to
large portions of the watershed is blocked or impeded by made-made barriers, such as dams or culverts.
Some of these improvements require addressing regulatory issues that may accompany restoration or
enhancement efforts. Instream flow conditions and some land-use practices may also need to be addressed
to support habitat improvements. While some fish passage and habitat improvement opportunities are
known, existing data gaps must be filled to develop more insight into the limiting factors for steelhead in
the watershed.
4.2.2 Watershed Erosion and Sedimentation
Erosion from various land-use practices is a common issue in many watersheds, and the Pilarcitos is no
exception. Sources of erosion are typically associated with agriculture, roads, trails and streamside
encroachment. Erosion and sedimentation issues can often be addressed with cost-effective Best
Management Practices.
Roads are a particular opportunity within the watershed. Road erosion has been cited by several of the
residents within the watershed as being at least partly responsible for flood-related damage. Road
maintenance issues were also noted during the tour of the upper watershed. Improved road design and
maintenance practices can improve hydrologic conditions, limit sediment delivery to the stream
environment, and prevent road failures.
4.2.3 Channel Maintenance
The Integrated Watershed Management Plan should address strategies for improving the natural channel
response functions in ways that can co-exist with other land-use needs. Channels are maintained by
natural flow conditions that present a certain frequency of relatively high flow events that can mobilize
and sort sediment. With a change in the natural balance of flooding, channels can become unstable over
time. While specific data is lacking, informal evidence in the Pilarcitos Watershed suggests that the
mainstem and several of the larger tributaries may be incised relative to their natural condition.
Encroachment of land-uses on channel banks, and the conversion of floodplains into agricultural fields
may also affect the channel condition.
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4.2.4 Riparian Vegetation and Habit
Riparian communities have a strong influence on the geomorphic and habitat functions for the stream
environment. The riparian canopy affects stream temperatures and aquatic plant growth. Instream wood
that naturally accumulates in the channel can support channel functions and can greatly benefit fish
spawning and rearing habitat. A functional riparian community often requires exposure to natural
disturbances that create new surfaces for the germination of native species and limited competition from
exotic invasive species. In the absence of these processes, riparian canopy species die without being
replaced by younger generations.
4.2.5 Control of Exotic and Invasive Vegetation
Invasive and non-native species have been documented in all 7 tributaries of the Lower Pilarcitos. These
species can present challenges for both ecosystem functions and desired land-uses. Exotic species prevent
recruitment of native vegetation. Invasive species are often “weedy” species that can infiltrate agricultural
fields, increase fire risk, and harm native species habitat requirements. Control of exotic species can be
resource intensive and usually requires a commitment of money and resources over a sustained period.
4.2.6 Lagoon Habitat
There is interest in restoring functional estuary conditions in the historic lagoon location. This idea has a
number of technical challenges. Sufficient inflows in excess of seepage through the sandbar are necessary
to maintain adequate habitat depth in the lagoon during the summer and fall. Potential structural
improvements to support a more functional lagoon are constrained by physical limitations at the site and
the risk of harming the timing and success of smolt migration. A restored lagoon may also need to address
high rates of predation, warm water temperatures, and water quality issues. There must also be sufficient
lagoon inflow to sustain a freshwater environment in the lagoon. Otherwise, a saltwater lens will develop
on the lagoon bottom and water temperatures may become too warm for steelhead. Overcoming these
issues will require a more focused analysis.
4.3 WATERSHED MANAGEMENT ISSUES
Human uses within the watershed are also an important consideration for the Integrated Watershed
Management Plan. Sustainable watershed management requires that land-use and management practices
are consistent with economic needs as well as ecological functions. This section briefly outlines some of
these issues.
4.3.1 Community Engagement
Community engagement and support are essential ingredients to success in implementing the
management plan. While the Pilarcitos Creek Restoration Workgroup offers an excellent opportunity to
involve key stakeholders, there is some concern about how best to involve the community at large in ways
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that can be productive and effective. Greater community involvement will help generate additional
support for the various projects recommended in the Preliminary Draft IWMP. Generally speaking, broad
public support can provide additional pressure on policy-makers and funding sources.
4.3.2 Beach Quality
The beaches near the Pilarcitos mouth have been documented as having some of the poorest water quality
in central California coast. It is unclear if this is an issue that should be addressed by the Integrated
Watershed Management Planning process. Sources of the poor water quality have not been specifically
identified. Some public perceptions point to large bird populations, insufficient streamflows, insufficient
sewage treatment, and urban runoff from the town of Half Moon Bay.
4.3.3 Landowner Concerns
Private landowner concerns vary widely. Many commercial and residential landowners have water rights
in the Pilarcitos watershed, and there is concern over the future of those rights. Landowners are also
concerned with upstream land management practices that may affect their land holdings, particularly as a
result of potential flood damage risks.
4.3.4 Landfill Issues
There continues to be concern about the effect of the landfill on watershed resources. Water quality may
be affected by the large population of birds associated with the landfill. There is also concern about the
long-term contamination of groundwater and alluvial water supplies downstream of the landfill.
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5. PRELIMINARY PROPOSED PROJECTS
This section describes various preliminary project ideas that address the issues described in Section 4, the
Updated Watershed Assessment (Appendix A), and data gaps identified by the consultant team. The
project list included in this section is considered preliminary and is subject to refinement before the Final
IWMP document is produced (by June 2008). Specific refinements will include:
• Evaluation of the project list using criteria described in Section 5.1 (upon approval of the
stakeholders)
• The inclusion of additional project ideas submitted by stakeholders
• Refinement of project descriptions and cost estimates to reflect appropriate levels of effort as
agreed to by the stakeholders through a collaborative process
• Factors associated with the Implementation Strategy (Section 6) that may affect any of the
proposed projects.
This preliminary list of proposed projects describes a series of planned activities that will benefit the
watershed and help achieve the goals and objectives described in Section 3. Four broad categories of
projects are presented here:
1. Improvement Projects – these projects include various actions that will have direct benefit
toward achieving plan goals and objectives. Improvement projects can include restoration,
enhancement, site acquisition projects and specific management action projects.
2. Feasibility Studies – these are studies that will support specific watershed improvements, but
require additional scientific or engineering analysis before a specific project plan can be
developed.
3. Planning Project Summaries – these are projects that would aid overall management of the
Pilarcitos watershed, but do not necessarily associate with a specific project. They may require
general regulatory review, planning and stakeholder collaboration projects.
4. Additional Assessment Projects – these projects include additional studies, data collection and
monitoring projects that are necessary to either develop specific improvement projects, guide
watershed management and planning activities, or to support adaptive management efforts.
5.1 PROJECT EVALUATION PROCESS
The consultant team has identified an objective project evaluation process that will be used to help rank
projects. Project rankings will be used as part of the process for identifying priorities, along with other
factors described below. We recommend an evaluation process as follows (Figure 2):
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1. Establish Recommended Criteria – this is completed and described in Section 5.1.1.
2. Stakeholder Review of Evaluation Criteria – In January 2008, we expect to receive feedback
from the stakeholders in the form of recommended revisions to the evaluation criteria.
3. Ranking Procedure – the consultant group and the stakeholder group will conduct project
rankings independently. To maintain anonymity, stakeholder rankings will be collected from each
stakeholder and reported as a combined ranking.
4. Ranking Reconciliation Process – the consultant group and the RCD will facilitate a discussion
about any significant differences between the stakeholder rankings and the consultant group
rankings.
5. Final rankings – will be developed by incorporating any appropriate adjustments to the rankings
provided by the two groups in response to the reconciliation process.
6. Other Factors – will be considered that are outside the specific evaluation criteria, but may be
relevant to project priorities. These can include:
a. The status of landowner cooperation
b. Project lead availability
c. Availability of funding
d. Regulatory considerations
e. Potential collaboration opportunities (e.g. alignment with specific stakeholder initiatives)
7. Final Priority List – a final project list will be developing incorporating all the information
described above.
5.1.1 Criteria for Project Priorities
Preliminary project priorities will be grouped into 5 classes based on the score identified from an
objective evaluation using core project criteria. Scoring will be achieved by rating each of the projects on
a scale of 1-5 (low to high) for each of the criteria described below, unless otherwise described. A
cumulative score for each project will be used to rank project priorities (Table 1), and project rankings
will be broadly grouped into classes. The criteria have been carefully selected to balance weighting
factors so that those projects most likely to successfully contribute to the goals and objectives will rank
higher than those with less potential benefit. The criteria are:
¾ Goals & Objectives – a score based on the number of objectives that could be addressed by each
project (Section 3 and Table 1).
¾ Estimated Benefit v. Cost – the project’s approximate value relative to cost.
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¾ Certainty of Benefits – our best professional judgment of the likelihood that project benefits will be
achieved as a result of the project. In most cases project benefits depend upon design factors that are
beyond the scope of this project to fully evaluate.
¾ Stakeholder Support – the level of support for the project by the stakeholders.
¾ Key Watershed Management Issues – the score describes the number of key watershed
management issues that will be addressed by the project (described in Section 4).
¾ Project Synergies – the degree to which the project creates disproportionately larger benefits when
combined with other projects or due to its location at a strategically important site within the
watershed. This category can also include cumulative effects benefits.
12/28/07 15
Table 1. Example Project Criteria Matrix. Actual values for each criteria and the specific weighting factors may vary during the
assessment process. Method is subject to review by stakeholders and facilitation by consultant team.
# of Key
Estimated Watershed
# of Goals & Benefit v. Certainty Stakeholder Management Project Total
Projects Objectives Cost of Benefits Support Issues Synergies Score
Weighting Factor 1.0 1.0 1.0 1.0 1.0 1.0
Improvement Project Summaries
Arroyo Leon Ponds Rehabilitation 13 5 5 4 6 4 37
Stone Dam Flow Releases 13 5 5 4 5 5 37
Remedial Action on the Lower Arroyo Leon Fish
Passage Project
Remedial Action on the Mills Creek Fish Passage
Project at the Historical Bridge
Modification of Barrier 1 on Lower Apanolio
Creek
Modification of Bongard’s Pond Operation and
the Channel Downstream
Modification of the 2007 Fish Passage Project at
Barrier 3 on Apanolio Creek
Apanolio Flashboard Dam and Apron Removal,
Downstream of the BFI Property Line
Lower Pilarcitos Streamflow Improvements
Erosion Control Projects 6 3 4 5 4 4 26
Stream Maintenance & Restoration Support
Fish Habitat Enhancement Opportunities
Feasibility Studies
Lagoon Restoration Feasibility Study
Pilarcitos Lake Dead Storage Access Feasibility
Study
Grey Water Utilization Study
Riparian Cons. Easement Program
12/28/07 16
Planning Project Summaries
Eucalyptus Control Planning
Watershed Monitoring Program
Additional Assessment Project Summaries
Water Budget Development Project(s)
Road Assessment Project 10 4 5 3 6 3 31
Geomorphic Channel Assessment
Arroyo Leon Fish Habitat Assessment
Fish Habitat Assessment
Riparian Habitat Restoration and Invasive Plant
Eradication Assessment
Assess Habitat Management and Restoration
Opportunities for Sensitive Wetland Species
Watershed-Scale Sensitive Plants and Habitats
Assessment
12/28/07 17
5.2 IMPROVEMENT PROJECT SUMMARIES
The following list of improvement projects is preliminary and based on the information available to the
consultant team.
5.2.1 Arroyo Leon Ponds Rehabilitation
Project Implementation Lead: TBD
Preliminary Cost Estimate: ~$50,000 for improvements. Uncertain cost for permitting and design. Initial
designs are available.
5.2.1.1 Project Summary

This project would restore existing instream ponds on Arroyo Leon Creek to provide better summer
rearing habitat for juvenile steelhead. Operation of these ponds was stopped by regulatory action after
2001 in response to concerns regarding fish passage and requirements under the Endangered Species Act.
The rehabilitation will include construction of overflow flumes suitable for steelhead smolt passage and
modification of the outlet structures on one or both Arroyo Leon Ponds (Johnson Ranch or Giusti) so that
they may be quickly drained prior to significant forecasted storm events. The rehabilitation process will
develop operational guidelines and/or structural improvements to minimize negative impacts while
restoring functional rearing habitat, and will secure permits from the California Department of Fish and
Game and the National Marine Fisheries Service to resume operation of the ponds in a manner that
provides steelhead rearing and does not significantly interfere with fish passage.
5.2.1.2 Project Benefits

This project will restore the most important previously-available steelhead rearing habitat within the
Pilarcitos Creek watershed under the historic water management regime through constructed features and
active management. Sampling within the ponds during their prior operation, suggests that it is likely that
they produced more steelhead smolts (and much larger smolts) than most of the remainder of the
Pilarcitos watershed. The on-channel ponds provide smolt densities approximately 10-20 times higher
than equivalent instream habitat, as measured in 2001. The habitat that could be recreated in these ponds
would mitigate the loss of rearing habitat that would have been provided by a functional lagoon at the
creek mouth that has been lost due to water diversion except in the very wettest of years. Winter diversion
to off-channel ponds may be a part of this project to ensure that operation of the on-channel ponds has
minimal impact to migrating or rearing steelhead. Restoration of the Guisti ponds would also enhance
habitat for the California red-legged frog (CRLF). CRLF were observed at these ponds during previous
fish surveys (Jerry Smith, pers. comm. 2007). The potential for CRLF breeding could be increased to the
extent that surface water impoundment could be initiated earlier in spring without compromising
steelhead migration.
12/28/07 18
5.2.1.3 Potential Project Collaboration Resources
• Peninsula Open Space Trust
• Giusti Farms
5.2.2 Stone Dam Flow Releases
Preliminary Cost Estimate: TBD

This project will provide spring and summer/fall flows below Stone Dam to improve adult steelhead
passage and summer rearing of juvenile steelhead in the 2 miles between Stone Dam and the Coastside
County Water District well field. The project will modify the water right to allow the recovery of all or a
portion of the dry-season bypass flows at the Coastside County Water District well field for water supply
purposes. It will evaluate and design infrastructure improvements that can support flow management and
will provide operational guidelines that direct flow releases and support water supply management
objectives

The project will improve adult steelhead passage and summer rearing for juvenile steelhead in a reach
with relatively good stream substrate conditions and that usually has low flows or becomes intermittent in
summer. The enhanced steelhead summer rearing habitat from this project below Stone Dam will mitigate
loss of steelhead habitat above Stone Dam.

• San Francisco PUC
• Coastside County Water District
5.2.3 Remedial Action on the Lower Arroyo Leon Fish Passage Project
Preliminary Cost Estimate: $150,000+

Reconstruct lower vortex weir under the Giovanoni driveway bridge by replacing the dislodged boulders
and constructing a more stable grade control structure downstream of the driveway weir and above the
downstream bend. Design modifications may include using grout or other approaches to stabilize existing
boulders. The design will address channel incision and establish slope protection along the right (north)
bank upstream of the weir. The design should also identify culvert and riparian vegetation improvements
12/28/07 19
to stabilize current hillslope failure and stream sedimentation. Hillslope toe protections may also be
necessary at the outside of the sharp bend immediately upstream of the driveway bridge.

This project will improve and maintain fish passage to the upper portion of Arroyo Leon over a wider
range of storm flows and prevent further erosion and sedimentation of the creek.

• Landowner- The Giovanonis
5.2.4 Remedial Action on the Mills Creek Fish Passage Project at the Historical Bridge

Reconstruct the failing boulder vortex weirs downstream of the historic bridge by designing stable weir
structures that can sustain the hydraulic forces below the culvert. Designs may include using grout or
other approaches to stabilize existing bouldersand the need to address leakage of flows at the weir to
maintain pool depth for fish passage. The project will improve the approach to the deteriorating lip of the
bridge culvert and backwater the culvert. It will also include construction of a low-flow channel inside the
culvert with baffling or grouted boulders.

This will be the 3rd attempt to provide adult steelhead passage past the historic bridge to at least a mile of
spawning and rearing habitat upstream. We do not judge it necessary to make the site passable to juvenile
steelhead, however.

• California Department of Parks and Recreation
5.2.5 Modification of Barrier 1 on Lower Apanolio Creek
Preliminary Cost Estimate: $150,000

Designs have been completed for boulder weir passage at the first barrier on Apanolio Creek to provide
passage past a diversion structure. The design should be re-evaluated to consider design stability based on
observations of similar boulder weir design failures on Mills Creek and Arroyo Leon. Design
12/28/07 20
modifications may include using grout or other approaches to stabilize the boulders used to form the
weirs.

Passage at this barrier will likely allow steelhead access upstream to near the BFI property line in wetter
years, including potentially rearing juvenile steelhead in the Bongard Pond (Barrier 2). Much of the
benefit depends upon operating the Bongard Pond for steelhead rearing, as the amount and quality of
accessible stream habitat is rather low. In general, the recommendations for Apanolio Creek barrier
modifications in PWA (1996) were based on the potentially high rearing potential in the pond and on the
expectation that habitat on BFI property was accessible and of relatively good quality. Assessment in
2007 (Alley 2007B) found relatively poor habitat and significant barrier problems just downstream of BFI
property and on the BFI property.

• Landowner-The Bongards
5.2.6 Modification of Bongard’s Pond Operation and the Channel Downstream

Modify the channel immediately downstream of the dam on Apanolio Creek to allow improved adult
steelhead access to the entrance into the inclined culvert through the dam. Guidelines for operation of the
dam should be designed to allow upstream adult steelhead passage, downstream smolt passage and
juvenile steelhead rearing within the pond.

If Barrier 1 is also modified, modifying the culvert for adult steelhead passage at this dam will allow
steelhead to spawn upstream of the dam and use the pond for juvenile summer rearing. Juveniles reared in
this pond can be expected to reach smolt size their first year and in greater numbers than may be produced
in the entire remainder of stream habitat in Apanolio Creek. Beneficial operation of the Bongard Pond for
steelhead rearing will also help mitigate the loss of valuable Pilarcitos lagoon habitat. Opening, closing
and filling of the dam/pond must be conducted in a manner to allow fish passage and juvenile rearing.

• Landowner - The Bongards
12/28/07 21
5.2.7 Modification of the 2007 Fish Passage Project at Barrier 3 on Apanolio Creek

The recently installed boulder weirs at Barrier 3 on Apanolio Creek are likely to fail based upon the
observations of similar structures on Arroyo Leon and Mills Creek in 2007. Observations of channel
widths upstream during our survey suggest that the reconstructed channel is likely to widen after storm
flows to at least 5 feet. Modifications may include using grout or other approaches to stabilize the existing
boulder weirs. Particular attention should be paid to the boulder weir stability and boulders keyed into the
streambanks. Evaluation should occur as soon as possible to prevent future boulder movement. The weirs
should be re-evaluated after a bankfull event to assess upstream fish passage opportunities, particularly at
the lowermost weir.

Modification of the recently installed weirs may prevent the failures observed with other ungrouted
boulder weirs in the watershed in wet years and will ensure steelhead passage past the new bridge after
downstream barriers have been removed. A relatively short stretch of stream is made available by this
project because of the conversion of the flashboard dam apron upstream (see 5.2.8) into a substantial
passage barrier by down-cutting below the apron in the last 10 years.

• Landowner - Gil Gossett
5.2.8 Apanolio Flashboard Dam and Apron Removal, Downstream of the BFI Property Line

Channel downcutting below the concrete apron at an unused flashboard dam has produced a nearly
impassable barrier to migrating adult steelhead. The apron should be removed to prevent further down-
cutting, and the channel grade should be stabilized.

This project would remove a fish passage barrier, reduce sediment production from further down-cutting,
and improve downstream habitat. If the downstream Barrier 1 is modified, this project would allow
steelhead access to an additional ½ mile of potential steelhead habitat of relatively low quality before
encountering the first of 4 barriers on BFI Property.
12/28/07 22
• Landowner - Gil Gossett
5.2.9 Lower Pilarcitos Streamflow Improvements

Projects that increase summer and fall stream flows to the lower Pilarcitos Creek and its estuary/lagoon
could resolve one of the primary limiting factors affecting habitat in the lower watershed. One approach is
described elsewhere (Stone Dam Flow Releases). Specific projects will be identified collaboratively
within the stakeholder group, and could include projects that:
• Improve the Stone Dam gate system to develop more automated flow regulation capacity and to
support more efficient flow management
• Develop efficient water transport and storage systems for more direct delivery to CCWD
• Augment instream flows with grey water sources OR substitute grey water for uses that currently rely
on instream flows
• Evaluate the purchase of water rights for dedicated use in maintaining minimum flows to the summer
lagoon
• Stormwater detention systems that are designed to support increased baseflows to the lower
watershed
• Increased off-channel storage facilities that can store water for summer release

A system of streamflow enhancements could improve fish habitat and water quality conditions in the
lower watershed.

• SFPUC
• CCWD
5.2.10 Erosion Control Projects
12/28/07 23
The project will identify and prioritize erosion control projects throughout the watershed using a
combination of aerial surveys, stream surveys, stakeholder interviews, and other methods. The focus of
the erosion control projects will be to reduce the level of fine sediment in the creek through source
control, onsite treatment and/or mitigation.

Erosion control projects can reduce the amount of fine sediment delivered to the stream, provide
improved habitat for aquatic and terrestrial species, and have a number of other potential benefits,
depending upon the specific site conditions. Existing information regarding potential project sites is
incomplete and largely anecdotal. A systematic inventory and assessment will support a more efficient
and effective resource for identifying specific project sites and priorities.

TBD
5.2.11 Stream Maintenance & Restoration Support

This project will provide technical guidance, technical support and funding in support of stream and
watershed maintenance issues throughout the Pilarcitos watershed.

This project will support community and stakeholder collaboration in watershed management. Example
projects might include establishing guidelines for consistent bank stabilization treatments that restore the
dynamic equilibrium of the creek on public and private land in the Pilarcitos Creek watershed.

TBD
5.2.12 Fish Habitat Enhancement Opportunities

This goal of this program would be to develop collaborative efforts with willing landowners to implement
instream enhancements for the benefit of fish. Specific opportunities might include habitat structural
12/28/07 24
improvements, large woody debris placement, passable grade control structures, etc. Specific attention
might be given to rearing habitat improvements or enhancements, or instream enhancement projects that
increase the storage and sorting of spawning gravels in reaches that can supply competent gravel.
Additional projects could evaluate upstream reaches on Mills, Arroyo Leon and upper Pilarcitos for
possible spawning gravel retention initiatives.

This program would increase fish habitat throughout the watershed by leveraging resources available to
willing landowners with guidance from expert staff. Under current conditions, rearing habitat is generally
limiting overall fish production.

• San Mateo Resource Conservation District
• Landowners
5.2.13 Other Enhancement Activities (template)
5.3 FEASIBILITY STUDIES
5.3.1 Lagoon Restoration Feasibility Study

This project would identify the specific opportunities and constraints for restoring a functional lagoon at
the mouth of Pilarcitos Creek. The study will evaluate existing and potential hydrologic conditions,
substrate conditions, and site geomorphology to identify any restoration potential.
12/28/07 25
Freshwater lagoons (closed sandbar) provide important summer rearing habitat for juvenile steelhead, and
open estuaries provide saltwater transition habitat for smolting steelhead in many coastal watersheds
(Smith 1990; Bond 2006). Estuaries can provide habitat for feeding by smolts migrating to the ocean in
late winter and spring and may provide a substantial spring growth increment to improve ocean survival.
In addition, deep pockets in open estuaries in spring can trap heavier salt water on the bottom during high
tides, to provide habitat where smolts can gradually adjust to salt water. However, in summer heavier salt
water behind the sandbar will trap heat on the bottom, producing an unsuitably warm lagoon subject to
water quality problems; sufficient freshwater inflow is needed to convert the lagoon to freshwater to
provide good steelhead habitat. In summation, significant hydrologic, geomorphic and ecological
constraints must be addressed before a viable lagoon restoration design can be developed.

TBD
5.3.2 Pilarcitos Lake Dead Storage Access Feasibility Study

This project will evaluate opportunities for accessing dead storage in Pilarcitos Reservoir that could be
used to improve overall water supply conditions for fisheries and other uses. Dead storage is the volume
of water that exists within Pilarcitos Reservoir below the water supply intake structures. Key factors that
need to be considered include the water quality in low limnological horizons within the lake, the cost and
feasibility of structural improvements, and the potential benefit to instream flows and/or general water
availability.

Access to what is presently dead storage could provide a significant stored water resource in support of
high summertime instream flows in Pilarcitos Creek below Stone Dam. Low summertime instream flows
have been identified as one of the critical limiting factors affecting fish habitat in lower Pilarcitos Creek.
5.3.3 Grey Water Utilization Study
12/28/07 26
This project would identify opportunities and establish the feasibility of developing a grey water
infrastructure within Pilarcitos watershed. The project would identify specific sources of grey water,
potential users, and treatment and delivery system options. The feasibility study will identify the
estimated reduction in virgin water demand that could be achieved by implementing a grey water system
and the estimated cost of design, permitting and development of the required infrastructure.

Adding grey water infrastructure within the Pilarcitos watershed could reduce demand for virgin water
supplies, potentially increasing the availability of fresh water for instream habitat uses. It could also
support greater capacity for beneficial uses of water within the Pilarcitos without increasing the need to
import water from other sources.

TBD
5.3.4 Riparian Conservation Easement Program Feasibility Study
Preliminary Cost Estimate: ~$10-15,000

This project would explore the feasibility of developing, expanding or applying a conservation easement
program within the Pilarcitos Creek Watershed. It would evaluate any existing easement projects within
the watershed and study examples of comparable programs featuring typical projects that demonstrate
potential for restoring riparian habitat on private land along salmonid bearing streams. It would
investigate current San Mateo County Ordinances and Local Coastal Program stipulations designed to
protect riparian habitat and identify any potential barriers to implementation of these regulations and
locate sites where the riparian corridor has been adequately protected through these measures.

A conservation easement program can provide opportunities for sustained landscape management benefits
while providing landowners appropriate compensation for applying conservation protections along their
lands.

• POST
• RCD
• Landowners
12/28/07 27
5.4 PLANNING PROJECT SUMMARIES
5.4.1 Eucalyptus Control Planning

This project will coordinate among regulating agencies to establish protocols in support of weed species
removal from riparian zones and adjacent habitats by willing landowners. The project will identify
regulatory and permitting guidelines, appropriate removal methods, and perhaps incentive programs, for
removal and control of eucalyptus.

Eucalyptus removal from riparian zones will have the following potential benefits:
• Improve native riparian habitat quality and quantity

• Increase native riparian habitat understory diversity
• Improve riparian habitat for native riparian obligate (often rare) bird species
• Improve soil conditions by potentially increasing permeability and decreasing runoff and erosion
• Increase inputs of high quality leaf litter into the aquatic food chain

• California State Parks
5.4.2 Watershed Monitoring Program

This program would establish a funding mechanism and support for routine watershed monitoring. The
Watershed Monitoring Program would establish a cost-efficient, systematic data collection strategy that
would address ongoing watershed management concerns. The program will also establish a rigorous
adaptive management framework to guide management decisions and provide feedback on existing
actions. The Watershed Monitoring Program would also assist in coordinating stakeholder collaboration
to address key impacts identified by the monitoring practices.
12/28/07 28
This program would support landowners and agencies by providing them with improved knowledge and
resources to guide watershed management. The program would complement and contribute to the
additional assessment projects (Section 5.5), and would be a resource to help guide additional data
collection efforts within the watershed.

• RCD
• SFPUC
• CCWD
• POST
5.5 ADDITIONAL ASSESSMENT PROJECT SUMMARIES
This section identifies key data gaps and describes the work required to fill them. This section outlines a
preliminary cost estimate for each of these Data Gaps, and the approximate timeline for filling the various
gaps. Costs depend on the project scope; these estimates include assumptions about the approximate level
of effort necessary. The level of detail necessary for each effort depends in large part on the proposed
management actions and opportunities that will be considered during the planning process (see Section
5.1). Data gaps with a large cost range reflect current uncertainty about the appropriate level of analysis
needed to address that issue. There are also some themes that were identified in more than one area that
could be made more efficient if efforts are combined such as those tasks associated with refining the
Water Budget.
5.5.1 Water Budget Development Project(s)

One of the key limiting factors in identifying and evaluating water supply improvements is considerable
uncertainty about the water budget for the Pilarcitos Watershed. A detailed water balance accounts for all
the sources and uses of water and typically addresses its availability throughout the watershed for wet,
normal and dry years. Many of the components for such an understanding are available, but several key
elements are missing. Components of a detailed water balance include (in order of priority):
a. Estimates of Diversions from Pilarcitos Reservoir to SFPUC – A detailed accounting of water

diversions from Pilarcitos Reservoir to other facilities operated by SFPUC (e.g., Crystal Springs
Reservoir) is not available. This fundamental data will help identify strategies for more efficient water
transfers and maintenance of instream flows for Pilarcitos Creek.
12/28/07 29
b. Review Existing Gage Data – Previous monitoring studies for several of the subwatersheds collected
streamflow data at 15-minute intervals. However, the published reports only provide summary results
that limit our ability to evaluate more detailed subwatershed response patterns. Compiling and
integrating this data into a watershed-scale hydrologic analysis could help inform the rainfall-runoff
transformation and baseflow conditions for these tributaries, which could help establish operational
strategies for managing flow releases below Pilarcitos Lake and Stone Dam.
c. Surface Water Hydrologic Model - Detailed hydrologic measurement or modeling of subwatersheds
will improve our understanding of annual flows, storm response, and baseflow conditions, especially
if this model can be calibrated to existing flow information. A model will allow analysis of various
different test scenarios to help identify the potential benefits and impacts associated with various
strategies.
d. Integrate Surface/Subsurface Models – understanding the interaction between stream conditions and
subsurface withdrawals will help establish sustainable limits to groundwater use, improved
management strategies for groundwater pumping given instream flow effects and can help improve
groundwater storage and conjunctive use strategies.
e. Estimates of Private Diversions - Improved estimates of actual (versus permitted) water rights
diversions will help to estimate the losses (reductions) associated with diversions as opposed to all
other loss mechanisms. In addition to evaluating permitted water rights, an estimate of private well
usage in the watershed on a monthly and annual basis would augment the water balance and help to
determine the cumulative level of impact from private well usage.
f. Perennial Flow Distribution for Dry Years – Determine spatial extent of perennial flow distribution
in dry years to help constrain estimates for the water balance associated with private users (for which
current data is unavailable) and to help develop an understanding of available fish rearing habitat.

A detailed water budget allows managers and stakeholders to quantify and identify the sources and uses
of water throughout the watershed. It will provide objective, numerical data to guide selection of project
priorities, identify potential problem areas, and forecast response to various proposed projects. A well-
maintained water budget will also allow water supply agencies to better coordinate responses to demand
needs and will support the development of improved monitoring and adaptive management tools.

TBD
5.5.2 Road Assessment Project
Preliminary Cost Estimate: $15-40,000 (assuming existing data can be integrated into this project)

A systematic road assessment project will evaluate and prioritize locations of significant hydrologic
impacts, sediment sources, and sediment delivery and impact to the channel network. The road
assessment will map and classify existing roads, assess and rate level of watershed impacts, identify
12/28/07 30
maintenance needs and recommend Best Management Practices. This effort will build on existing studies
by SFPUC, California State Parks, Peninsula Open Space Trust, and others, by integrating and
synthesizing the information for a complete watershed-scale understanding of the impacts from roads on
fish habitat, erosion risk and water quality. The assessment will focus on dirt roads, private roads, local
roads and county roads.

The road inventory and assessment will identify and prioritize sources of sediment and significant
hydrologic impacts associated with roads. Roads are typically one of the largest sources of fine sediment
pollution. Erosion from cutslopes and bare road surfaces is easily routed to the road drainage system,
which is often connected to the stream environment during large storms. Road drainage systems can
destabilize roads fillslopes causing landslides. Hydrologic effects from road can also have significant
impacts to both peak flows and baseflows. Several anecdotal citations and consulting team observations
of road problems were noted during the watershed assessment update process.

• SFPUC
• POST
• California State Parks
• RCD
5.5.3 Geomorphic Channel Assessment
Preliminary Cost Estimate: $25-40,000

An updated and systematic inventory of riparian and channel bank conditions could be developed along
the mainstem Pilarcitos Creek and targeted tributaries to identify habitat potential, sediment sources, and
channel stability conditions. This project will establish baseline conditions in support of stream habitat
improvements, channel incision risk assessment, streamside vegetation improvement opportunities,
sediment sources, and existing infrastructure impacts.

A systematic inventory of stream reaches will provide the technical basis to identify and manage
watershed impacts, establish project priorities, and evaluate cumulative watershed effects. The assessment
will be used to help identify the cost, benefits and level of effort necessary to meet IWMP objectives at
specific project locations throughout the watershed.
12/28/07 31
TBD
5.5.4 Arroyo Leon Fish Habitat Assessment

This assessment will fill the major data gap on fish habitat within the Pilarcitos Creek watershed. The
entire length of Arroyo Leon upstream of the modified barrier, especially upstream of Higgins-Purisima
Road, should be surveyed. Field data collection should depend upon the RCD obtaining access to this
stream reach. This includes approximately 2.5 miles of stream channel, and would entail walking the
reach until a natural barrier to anadromy is found. Habitat typing (evaluating habitat conditions) and
electrofishing to determine fish densities should be done in 3 selected segments/sites.

The extent and quality of upper Arroyo Leon habit will be known for the first time. This will allow proper
assessment of benefits of barrier projects downstream, and potential provide information on additional
potentially benefit projects in the Arroyo Leon watershed.
5.5.4.3 Potential Collaboration Resources

• POST
• Landowners
5.5.5 Fish Habitat Assessment

This project will improve habitat and fisheries evaluations throughout the watershed to address variations
in flow conditions associated with the existing data. Much of the habitat and fisheries evaluation for the
Pilarcitos Creek watershed was done in 1995, a very wet year. Subsequent evaluations were done in a
variety of rainfall year types: 1996, 1999, 2000, 2001, 2004 (average year) and 1998 (very wet/El Niño
year). In addition, the 1998 El Niño storms and the storms in 2005 and 2006 could have substantially
changed habitat conditions within the watershed. Components of such a systematic survey should identify
limiting factors affecting overall habitat quality, and prioritize specific restoration opportunities. The
project should specifically include the following:
12/28/07 32
a. Fish densities and sizes should also be re-evaluated at sites throughout the watershed in a single
(average) year, especially since surveys on Apanolio Creek (Alley 2007B) and the barriers on Mills
and Arroyo Leon (Alley 2007A) indicate substantial channel changes since the original surveys.
Ideally, fish densities and sizes should be re-evaluated during the same year that habitat conditions
are evaluated through electrofishing. The stream above Stone Dam should be studied because past
work there was not coincidental with sampling below Stone Dam. At least three habitats should be
sampled for juvenile steelhead in each habitat typed segment to determine an index of juvenile
steelhead density, habitat usage and growth rate. These data should be compared to fish data collected
in 1995-96 for the 1996 plan and subsequent sampling in Albert Canyon and above and below Stone
Dam. A report should be provided, summarizing updated qualitative steelhead densities, age/size
structure and habitat use compared to earlier findings.
b. Habitat conditions within reaches throughout the watershed should be re-evaluated for channel and
bank conditions, substrate composition, meso-habitat (pool, riffle, run) frequency, average pool
quality, escape cover, canopy, woody debris in the channel and potential wood recruitment, etc., such
as by habitat typing and evaluation in a 0.1 mile section in each reach. Habitat should be evaluated in
12, 0.15-mile stream segments distributed throughout the watershed. Habitat typing data should be
collected, including water depth, escape cover, substrate embeddedness (visual estimate), percent
fines (visual estimate) and tree canopy closure. Incidence of wood in the creek and streambank
erosion should be documented for each segment. Sources of large wood recruitment should be
inventoried in at least one 200-foot segment of each of the 0.15-mile habitat typed segments.
c. The lagoon area should be observed in a general fashion. Past work has indicated that it is usually dry
by late summer or even sooner and is likely to have surface water only intermittently. It is not
believed to have fishery value under the present water diversion scheme on the creek. If there happens
to be surface water at the lagoon during data collection at stream sites, then size, water depth and
presence/ absence of fish escape cover should be measured and photographs should be taken.

The project would provide a relatively complete baseline of information to assess and prioritize fish
habitat restoration opportunities in the watershed. The surveys will provide important information about
the status of fish habitat and population conditions in each of the identified sub-watersheds, as well as the
overall watershed. It will also identify and prioritize specific restoration opportunities.

TBD
5.5.6 Riparian Habitat Restoration and Invasive Plant Eradication Assessment
Preliminary Cost Estimate: ~$450,000
12/28/07 33
This project is the first step toward identifying and prioritizing riparian habitat restoration actions within
the watershed. As such, this project will first fill existing data gaps regarding the distribution of native
and invasive riparian habitats and species. It will then identify and prioritize riparian habitat restoration
and invasive plant eradication opportunities/projects. To fill existing data gaps, this project will survey
riparian habitat and invasive plants streamside corridors of the headwater region in Apanolio Creek,
Corinda Los Trancos Creek, Nuff Creek, Madonna Creek, Mills Creek, and Arroyo Leon Creek. The
project will characterize the riparian plant community, estimate riparian corridor widths, and map
invasive plant species to a similar level of detail presented in the Pilarcitos Creek Restoration Plan (PWA
1996). Methods would be similar to those used for the 1996 plan, namely color aerial photography
interpretation (using NAIP 2005 aerial imagery; see
http://datagateway.nrcs.usda.gov/GatewayHome.html) and some field surveys. The project will include
assessing the historical condition/width of the riparian corridor from examination of historical aerial
imagery to aid in the development of restoration goals. The products of this project would include the
identification of property ownership and prioritization of specific riparian restoration opportunities.
Such opportunities could generally include:
• Restore ecosystem processes that support the life-cycle requirements for native canopy species like
willow and alder
• Identify setback distances that support stable bank and riparian conditions
• Establish and fund a sustained program to manage exotic invasive species removal and native species
establishment
• Remove eucalyptus from riparian areas and replace with native canopy species (e.g. willow, alder,
etc)
This project would also prepare a user friendly brochure for landowners on the impacts, eradication
methods, and permitting requirements for the various riparian, invasive plants in the watershed

The project would provide a relatively complete baseline of information to assess and prioritize riparian
habitat restoration opportunities in the watershed. These reaches were not covered in the Pilarcitos Creek
Restoration Plan (PWA, 1996). The surveys will provide important information about the status of
riparian conditions in the identified sub-watersheds, and will identify and prioritize specific riparian
habitat restoration opportunities. It will identify specific riparian restoration/invasive plant eradication
projects. Information about the historical condition of riparian forest would be used to develop restoration
goals for riparian areas in the watershed.
12/28/07 34
• POST
• SFPUC
• RCD
• Others?
5.5.7 Assess Habitat Management and Restoration Opportunities for Sensitive Wetland Species
Preliminary Cost Estimate: ~$50,000

Little is known about the distribution and condition of suitable habitats for California red-legged frog
(CRLF), San Francisco garter snake (SFGS), and western pond turtle (WPT) in the watershed. This
project will collect the necessary information to determine habitat management/enhancement and
restoration opportunities in the watershed for these species. Such habitat enhancement and restoration
would also benefit numerous other associated aquatic and wetland species in the watershed. The project
will first involve conducting reconnaissance-level surveys to assess the suitability and quality of existing
pond and reservoir habitats in the watershed for CRLF, SFGS, and WPT. Reconnaissance-level surveys
(not protocol-level surveys at this planning stage) would then be conducted in suitable habitats for CRLF,
SFGS, and WPT, as well as for their predators and other threats to these species that might limit their
distribution, within primary habitat (i.e., ponds, pools within streams, and wetlands) throughout the
Pilarcitos watershed. This reconnaissance-survey information will then be synthesized to identify specific
habitat management and restoration opportunities throughout the watershed.

The project will result in a set of specific projects for improving habitat conditions for sensitive aquatic
species within the watershed.

• San Mateo County (possible HCP component?)
• SFPUC
• ?
5.5.8 Watershed-Scale Sensitive Plants and Habitats Assessment
Preliminary Cost Estimate: $5-10,000
12/28/07 35
This project will list sensitive habitats and special-status plant species that are either known to occur or
have the potential to occur within the entire Pilarcitos watershed, including areas outside of riparian areas.
The project will research the habitat requirements of special-status plant species, the site requirements for
sensitive habitats, and management concerns for each element. It will conduct reconnaissance surveys of
likely areas within the lower watershed and the headwater regions in Apanolio Creek, Corinda Los
Trancos Creek, Nuff Creek, Madonna Creek, Mills Creek, and Arroyo Leon Creek to determine the
location of sensitive habitats.

There are a number of sensitive habitats and special-status plant species in the watershed outside of the
riparian zone that were not considered in the 1996 PWA report that have value and warrant management
consideration (e.g., serpentine grassland, old-growth Douglas fir, maritime chaparral). The spatial extents
of these habitats are mapped in detail for the upper watershed, but their boundaries beyond SFPUC land
are not known. This project will support more specific habitat mapping projects as deemed appropriate.

• San Mateo County (possible HCP component?)
• SFPUC
• ?
12/28/07 36
6. IMPLEMENTATION STRATEGY
The implementation of the IWMP will continue to be driven by the Memorandum of Understanding
(MOU) (Appendix B) and the collaboration among IWMP stakeholders. This section will describe the
implementation strategy elements that will be developed over the next several months in response to a
more complete project list and identification of project priorities.
6.1 LEAD AGENCY RESPONSIBILITIES
Lead agencies will be responsible for developing assigned projects. Development may include obtaining
necessary funds, administering contracts, supervising project development, leading collaboration efforts,
and communicating with relevant partners and stakeholders.
6.2 FUNDING SOURCES
This section will identify potential funding sources for each project. It will include how well each project
can meet the funding priorities of known grant opportunities.
6.3 MILESTONES
Implementation milestones will be developed for the Final IWMP document, and will reflect the project
priorities.
6.4 MONITORING & ADAPTIVE MANAGEMENT
A monitoring and adaptive management approach will be described for the final IWMP. The purpose of
the monitoring and adaptive management program will be to:
• Assist in the development of adaptive management approaches for each project

• Fill critical data gaps that inform watershed management practices and decisions
• Establish and fund monitoring and adaptive management systems that measure the success of specific
watershed management strategies and guide appropriate responses
• Establish systems and processes for sharing data and information
• Establish a regulatory process that reduces the administrative burden associated with beneficial
IWMP projects
The program will utilize several components, including:
12/28/07 37
6.4.1 Implementation Monitoring
Implementation monitoring measures the extent that project design and intent is met by project
implementation. It usually is conducted shortly after implementation, and is guided by the specific design
documents developed for the project.
For example, if the project design calls for enhancement of 3 instream pools, then the implementation
monitoring action verifies that 3 pools were indeed made deeper with more escape cover than the pre-
existing habitat.
6.4.2 Effectiveness Monitoring
Effectiveness monitoring is a more comprehensive monitoring approach that evaluates how well the
implemented action achieves the desired results. It usually requires prolonged period of monitoring and
tracking over time.
For example, if the basis for the project design was that additional pools would improve rearing habitat
and produce a higher population of smolts, then the effectiveness monitoring protocols would measure
densities of smolt-sized juvenile steelhead in the newly enhanced pools in relation to densities in this
stream segment prior to pool enhancement and in comparison to other pools in the vicinity at the time the
newly enhanced pools are sampled. One would also measure the persistence of the pools over time.
6.4.3 Validation Monitoring
Validation monitoring involves testing specific working hypotheses that guide land management. A well-
designed monitoring program will integrate data collection protocols between effectiveness and validation
monitoring and will use validation monitoring to continuously refine performance measures and resources
objectives.
6.4.4 Resource Objectives & Performance Measures
Resource objectives are specific and quantifiable targets that can be used to guide management. When
resource objectives are met, then overall watershed management with respect to that resource is
considered to be in good shape. An example of a resource objective is an average annual smolt production
of X.
Performance measures are cost-effective ways to measure resource objectives. Using the example from
above, it may not be cost effective to measure every outmigrating smolt. However, a sample protocol (or
proxy variable) that is related to the number of smolts (but easier to measure) might be a more effective
monitoring metric (e.g., numbers of redds).
12/28/07 38
7. REFERENCES
Alley, D. W. 2007a. Apanolio Creek fishery assessment December. Prepared for this project.
Alley, D. W. 2007b. Evaluation of present condition of past fish passage improvement projects on Arroyo
Leon and Mills Creeks. Prepared for this project.
Bond, M. H. 2006. The importance of estuarine rearing to Central California steelhead (Oncorhynchus
mykiss) growth and marine survival. M. A. Thesis. University of California, Santa Cruz.
PWA (Philip Williams & Associates, Ltd.) (with Habitat Restoration Group, Prunuske Chatham and
Callander Associates). 1996. Pilarcitos Creek Restoration Plan. Prepared for Regional Water
Quality Control Board and California Department of Fish and Game. Report no. 1021.
Smith, Jerry, 2007. Personal Communication. Fisheries biologist and member of the consultant team.
Smith, J. J. 1990. The effects of sandbar formation and inflow on aquatic habitat and fish utilization in
Pescadero, San Gregorio, Waddell and Pomponio creek estuary/lagoon systems 1985-1989.
Report to California Department of Parks and Recreation.
12/28/07 39
8. LIST OF PREPARERS
This report was prepared by the following PWA staff:
Adam Parris, Project Manager

Setenay Bozkurt, Fluvial Geomorphologist
Elizabeth Andrews, PE, Project Director
Catherine Lee, Production Manager
With:
Mike Liquori, Senior Plan Writer/Geomorphologist, Sound Watershed Consulting

Max Busnardo, Restoration Ecologist, H. T. Harvey and Associates
Matthew Ramsay, Restoration Ecologist, H. T. Harvey and Associates
Don Alley, Fisheries Biologist, D.W. Alley & Associates
Jerry Smith, PhD, Fisheries Biologist, D.W. Alley & Associates
Joe Hayes, Hydrogeologist, Weber-Hayes and Associates
12/28/07 40
9. FIGURES
Figure 1. Pilarcitos Watershed Map
Figure 2. Evaluation Process Flowchart
12/28/07 41
Pilarcitos Reservoir
Project Location
e l
nn
Tu
s
c ito Lower Crystal Springs Reservoir
lar
Pi
Stone Dam
Skyline Quarry
Nu
Co rri nd a Lo
ff C Upper Crystal Springs Reservoir

re e
Alb
k
e
rt C
s Tr
any
an
Ap
on
co
no
a
s
lio
Cree
k
ek
re
k
sC
ee
c ito
Cr
ar
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l
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Pilarcitos Drainage Network

Headwater Drainage
Second Order
Third Order
n
o
Le
Fourth Order (Tributary)

Ar r o yo
Fifth Order (Perrennial)
Source: USGS (DRG, DEM), SFPUC (water bodies)

Note: Headwater drainage is defined as a first order stream. figure 1
Drainage area for this class ranges from approximately 20 - 80 acres.
±
Pilarcitos IWMP
Miles PWA Ref. # 1884
0 0.5 1 2
\\Sfo1\GIS\Pilarcitos\Figures\DrainageNetwork.mxd
Appendix A
PILARCITOS INTEGRATED WATERSHED MANAGEMENT PLAN
WATERSHED ASSESSMENT UPDATE
Watershed Assessment Update
Appendices
December 31, 2007
Pilarcitos Integrated Watershed

Management Plan
Prepared for
Prepared by
with Sound Watershed Consulting, H.T. Harvey & Associates, PWA

PHILIP WILLIAMS & ASSOCIATES, LTD.
D.W. Alley & Associates, Jerry Smith, PhD, and Weber-Hayes & Associates ENVIRONMENTAL HYDROLOGY
Pilarcitos Integrated Watershed Management Plan
Prepared for
Prepared by
with
Sound Watershed Consulting

H.T. Harvey & Associates
D.W. Alley & Associates
Jerry Smith, PhD
Weber-Hayes & Associates
December 31, 2007
PWA REF. # 1884 - T3A

Services provided pursuant to this Agreement are intended solely for the use and benefit of
the San Mateo Resource Conservation District.
No other person or entity shall be entitled to rely on the services, opinions,

recommendations, plans or specifications provided pursuant to this agreement without the
express written consent of Philip Williams & Associates, Ltd., 550 Kearny Street, Suite
900, San Francisco, CA 94108.
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Assessment Update.doc
12/28/07
TABLE OF CONTENTS
Page No.
1. BACKGROUND 1
2. EXECUTIVE SUMMARY 3
2.1 HYDROLOGY 3
2.2 GEOMORPHOLOGY 3
2.3 RIPARIAN ECOLOGY 4
2.4 WILDLIFE HABITAT 4
2.5 IMPLEMENTATION STATUS AND PROGRESS SUMMARY 5
3. HYDROLOGY 6
3.1 DATA SOURCES & METHODS 7
3.2 INSTREAM FLOWS 8
3.2.1 Pilarcitos at Half Moon Bay 8
3.2.2 Pilarcitos at Stone Dam 9
3.2.3 Contribution from Tributary Streams 10
3.2.4 Hydrologic Effect of Eucalyptus Globulus 13
3.3 REVIEW OF WATER SUPPLY RESOURCES 13
3.3.1 San Francisco Public Utilities Commission 14
3.3.2 Coastside County Water District 15
3.3.3 Other Water Rights 16
3.4 GROUNDWATER RESOURCES 17
3.4.1 Upper Pilarcitos 17
3.4.2 Middle Pilarcitos 18
3.4.3 Lower Pilarcitos 18
3.5 WATER QUALITY 19
3.5.1 Water Treatment Facilities 19
4. GEOMORPHIC CONDITIONS 21
4.1 DATA SOURCES AND METHODS 21
4.2 WATERSHED GEOLOGY 22
4.2.1 Landslides, Debris Flows and Hillslope Erosion 22
4.2.2 Land Use Impacts 25
4.2.3 Channel Form and Erosion 28
4.2.4 Sediment Discharge Rates 29
5. RIPARIAN ECOLOGY 31
5.2 DISTRIBUTION AND COMPOSITION OF NATIVE PLANT ASSOCIATIONS 32
5.3 INVASIVE PLANT SPECIES 34
5.4 SENSITIVE PLANT COMMUNITIES 35
5.5 SPECIAL-STATUS PLANT SPECIES 35
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12/28/07 i
6. WILDLIFE HABITAT 41
6.2 STEELHEAD 41
6.2.1 Flow Diversions 42
6.2.2 Culverts and Fish Passage 43
6.2.3 Rearing Habitat 43
6.2.4 Stream Habitat Summary 46
6.3 HERPETOFAUNA 56
6.3.1 California Red-legged Frog 57
6.3.2 San Francisco Garter Snake 58
6.3.3 Western Pond Turtle 59
6.3.4 Discussion of Herpetofauna 60
6.4 BIRD SPECIES 60
6.4.1 Marbled Murrelet 61
7. IMPLEMENTATION STATUS AND PROGRESS SUMMARY: 1996 RESTORATION PLAN64
7.1 MAINTAIN UNPAVED ROADS 67
7.2 REMOVE EXOTIC PLANTS AND REPLACE WITH NATIVE SPECIES 67
7.3 MODIFY BARRIER AND STABILIZE BANKS AT HISTORIC BRIDGE ON MILLS
CREEK AND AT DIVERSION DAM 67
7.4 MODIFY FISH PASSAGE BARRIERS AND STABILIZE BANKS ON APANOLIO
CREEK 68
7.5 INSTALL VORTEX WEIRS ON PILARCITOS CREEK 69
7.6 INCREASE INSTREAM FLOW TO ESTUARY 69
7.7 FISH BARRIER MODIFICATION OR REMOVAL ON ARROYO LEON 69
7.7.1 Severe Culvert Barrier 69
7.7.2 Johnson Ranch (“Giusti Farms”) Dams and On-Channel Ponds 70
8. REFERENCES 73
9. LIST OF PREPARERS 80
10. FIGURES 81

12/28/07 ii
LIST OF APPENDICES
Appendix A. Geospatial Map Inventory

Appendix B. Oral Histories Pertaining to IWMP
LIST OF TABLES
Table 1. Pilarcitos Creek Subwatershed Characteristics 6

Table 2. Available Data for USGS Gages in the Pilarcitos Watershed 7
Table 3. Annual Rainfall Statistics for Pilarcitos Dam and Half Moon Bay Weather Stations 8
Table 4. Typical Wetted Channel Dimensions During Site Discharge Measurements 9
Table 5. Average monthly flow conditions for Pilarcitos Creek 10
Table 6. Estimated Annual Water Budget 12
Table 7. Summary of Permitted Appropriative Diversions and Statement of pre-1914 Diversions 17
Table 8. Convergent Channel Network 24
Table 9. Land Use Change and Associated Hydrologic and Geomorphic Effects 27
Table 10. Preliminary Estimate of Normalized Bedload Production Rate 30
Table 11. Preliminary Estimate of Normalized Suspended Load Production Rate 30
Table 12. Conservation Status, Habitat Information, and Occurrence Records of Special-Status Plant
Species Reported from the Vicinity of the Pilarcitos Creek Watershed within Riparian
Habitats 37
Table 13. Existing Steelhead Rearing, Spawning and Migration Conditions for Stream Reaches in
Pilarcitos Creek Watershed. 47
Table 14. Status Summary of Recommended Alternatives from 1996 Restoration Plan 65

12/28/07 iii
LIST OF FIGURES
Figure 1. Pilarcitos Drainage Network

Figure 2. Mean Annual Rainfall in the Pilarcitos Watershed
Figure 3. Total Annual Precipitation at Half Moon Bay
Figure 4. Total Annual Precipitation at Pilarcitos Dam
Figure 5. Median Monthly Precipitation Variation at Half Moon Bay
Figure 6. Daily Precipitation Variation at Pilarcitos Dam
Figure 7. Pilarcitos Streamflow at Half Moon Bay
Figure 8. Total Annual Discharge from Pilarcitos Creek at Half Moon Bay
Figure 9. Annual Hydrograph for Pilarcitos Creek at Half Moon Bay
Figure 10. Peak Instantaneous Discharge at Half Moon Bay
Figure 11. Peak Annual Discharge (Log Pearson III)
Figure 12. Annual Days with Zero Recorded Flow at Half Moon Bay
Figure 13. Rating Curve for Pilarcitos Creek near Half Moon Bay
Figure 14. Rating Curve Shift Adjustment for Pilarcitos Creek near Half Moon Bay
Figure 15. Pilarcitos Streamflow at Stone Dam
Figure 16. Annual Hydrograph for Pilarcitos Creek below Stone Dam
Figure 17. Rating Curve for Pilarcitos Creek below Stone Dam
Figure 18. Streamflow Gain Between Stone Dam and Half Moon Bay
Figure 19. Proportion of Flow from Lower Watershed
Figure 20. Annual Flow Exceedance Pilarcitos at Half Moon Bay
Figure 21. Water Supply Network
Figure 22. Water Diversions from 1996 to 2007
Figure 23. Geologic Units and Surface Deposits
Figure 24. Soil Particle Size
Figure 25. Hillslope Failure and Channel Erosion
Figure 26. Channel Grade Summary
Figure 27. Watershed Slope
Figure 28. Partial Road Map
Figure 29. Stream Gradient in the Pilarcitos Watershed
Figure 30. Annual Peak Discharge Probability Pilarcitos Creek at HMB
Figure 31. California Wildlife Habitat Relationship (CWHR) Vegetation Data
Figure 32. Locations of Riparian Plant Communities and Eucalyptus Groves (South)
Figure 33. Locations of Riparian Plant Communities and Eucalyptus Groves (North)
Figure 34. Locations of Significant Concentrations of Invasive, Non-native Plant Species (South)
Figure 35. Locations of Significant Concentrations of Invasive, Non-native Plant Species (North)
Figure 36. Vegetation Communities
Figure 37. California Natural Diversity Database (CNDDB) Plant Records
Figure 38. California Natural Diversity Database (CNDDB) Animal Records
Figure 39. Marbled Murrelet Habitat / Occurrences

12/28/07 iv
1. BACKGROUND
The Pilarcitos Creek watershed, located in the steep coastal hills of San Mateo County, California (Figure
1), covers a 28-square-mile area originating on the east side of Montara Mountain above the City of Half
Moon Bay. The watershed encompasses seven subwatersheds containing the following smaller tributaries:
Nuff Creek, Corinda Los Trancos Creek, Apanolio Creek, Albert Canyon, Madonna Creek, Mills Creek,
and Arroyo Leon. Pilarcitos Creek can be divided into three broad reaches: Upper Pilarcitos, above the
confluence with the seven tributaries; Middle Pilarcitos, primarily confined to an agricultural and
residential floodplain valley; and Lower Pilarcitos, which flows through the City of Half Moon Bay to the
Pacific Coast (Figure 1).
The Pilarcitos Creek watershed is host to a number of plant and animal species, including steelhead trout,
that are listed as “threatened” by the Federal government (PWA 1996, RCD 2007b). Over recent history,
physical and biological impacts resulting from human activity have degraded the overall watershed
condition, threatening native plant and animal species including steelhead (PWA 1996, RCD 2007b). In
addition, water demand has increased with the growth of residential, agricultural, and industrial
development in the Pilarcitos Creek watershed, decreasing the amount of water available for surface flow
in streams. Activities impacting watershed health include:
agricultural land-use along creek floodplain and riparian corridors;

water supply management including operation of two large dams, many smaller instream
diversions, and several groundwater extraction well systems;
a large landfill operation;
local sand and gravel operations;
urbanization; and
transportation corridors (e.g., roads).
The San Francisco Public Utilities Commission (SFPUC) owns a majority of the lands in the Upper
Pilarcitos region and has stored water in two locations within the watershed since 1910: Pilarcitos Lake
behind Pilarcitos Dam, and a very small reservoir behind Stone Dam (Freeman 1912, RCD 2007b).
Below the dams, the watershed includes a mix of public and private lands, including agricultural areas.
Public landowners include the Coastside County Water District (CCWD), the City of Half Moon Bay
(HMB), California State Parks (State Parks), and the Sewer Authority Mid-Coastside (SAM).
These public and private stakeholders have been working intermittently together since the mid-1990s as
part of the Pilarcitos Creek Watershed Restoration Project funded by the California Department of Fish
and Game (CDFG) and the San Francisco Regional Water Quality Control Board (RWQCB). The
Pilarcitos Creek Advisory Committee (PCAC) was formed to advise the CDFG and RWQCB with the
Restoration Project. In 1999, the San Mateo Resource Conservation District (RCD) became responsible

12/28/07 1
for implementing the 1996 Restoration Plan (PWA 1996). The PCAC continued in its role as advisor and
stakeholder advocate of issues concerning Pilarcitos Creek.
Members of the PCAC and other stakeholders formed the Pilarcitos Creek Restoration Workgroup
(Workgroup), which aims to implement restoration and management actions in the Pilarcitos watershed.
The Workgroup, with funding and support from the RWQCB and SFPUC, is developing an Integrated
Watershed Management Plan (IWMP) with the assistance of the present consultant team. The RCD is
acting as the contact manager and convener of the Workgroup meetings. The goal of the IWMP is to
restore steelhead trout and other native plant and animal species in the riparian community while
minimizing the potential impacts to public health, water supply, and other beneficial uses and economic
interests (RCD 2007b).
The Updated Watershed Assessment is a synthesized update of the information provided in the
Restoration Plan (PWA 1996) and subsequent studies. This introduction comprises Chapter 1 of the
Assessment. Section 2 is a brief overview of watershed processes which provides context for evaluating
existing watershed conditions. Section 3 provides a description of the existing watershed conditions.
Finally, Section 4 summarizes the prioritized alternatives recommended in the 1996 Restoration Plan and
provides information on the status and progress of implementation of the Plan.
A spatial inventory of geographic information systems (GIS) data is located in Appendix A, and oral
histories pertaining to the watershed description are included in Appendix B.

12/28/07 2
2. EXECUTIVE SUMMARY
This document provides an update of the description of the Pilarcitos Watershed provided in the 1996
Restoration Plan. Below, key aspects of the watershed description provided by this document are
summarized.
2.1 HYDROLOGY
The Pilarcitos Creek watershed encompasses 28 square miles in the steep coastal hills above the City of
Half Moon Bay, CA in San Mateo County. Pilarcitos Creek originates on the east side of Montara
Mountain and is divided by seven subwatersheds containing the following smaller tributaries: Nuff Creek,
Corinda Los Trancos Creek, Apanolio Creek, Albert Canyon, Madonna Creek, Mills Creek, and Arroyo
Leon. Recorded precipitation values range from a low of 13.1 inches per year to a high of 65.5 inches per
year. A majority of the subwatersheds receive a mean annual precipitation of approximately 33 inches.
The hydrologic conditions are highly variable within the watershed, and stream flows are significantly
impacted by flow diversions for both local and regional purposes. Pilarcitos Reservoir and Stone Dam
(built circa 1900) have modified flow dramatically, eliminating all of the summer flows from the upper
watershed in most years. Hydrologic modification of tributaries (e.g., Corinda de las Trancas) has also
modified surface flows in the lower watershed. Section 3 provides detailed hydrologic data for each of the
sub-watersheds in the Pilarcitos system.
2.2 GEOMORPHOLOGY
Stream channel geomorphology is determined by the runoff and sediment characteristics of a watershed.
In a stable stream channel, runoff and sediment are in balance and the channel neither erodes nor aggrades
over time though channel will adjust dynamically to individual runoff events. When watershed runoff or
sediment characteristics are altered rapidly by human activity, stream channels are often unable to adjust
quickly enough to maintain a stable configuration. Throughout the Bay Area, many stream channels have
responded to development-induced runoff increases by “incising” into the landscape, so that flood flows
are not able to access the surrounding floodplain. Stream flow reductions due to dams and/or diversions
also have the potential to affect long-term channel morphology, causing excessive deposition and/or
channel braiding. Dams can also reduce sediment supply by trapping coarse sediment, causing or
exacerbating channel erosion in the downstream channel.
Channels throughout the Pilarcitos watershed are incised, possibly due to long-term land-use impacts that
have altered flow patterns, contributing to higher peak flows. Streamside riparian management may also
play a role in reducing bed stability within the watershed. An evaluation of sediment sources and
transport indicates that the two primary sources of sediment in the Pilarcitos
Watershed are Apanolio Creek and Upper Pilarcitos Creek below Stone Dam. Section 4 provides a more
detailed summary of geomorphic and sediment transport characteristics of the Pilarcitos watershed.

12/28/07 3
2.3 RIPARIAN ECOLOGY
The riparian plant community native to the Pilarcitos watershed includes of a wide diversity of native
plant species, including alders, willows, and bigleaf maples. Historically, the vegetation structure
included a riparian tree over story, a shrub layer and a dense herbaceous layer with no bare ground,
supporting diverse and abundant wildlife. Healthy riparian vegetation can also help to stabilize stream
banks and reduce inputs of sediment to the streams from bank erosion or by acting as a filter for sediment
from upslope or adjacent land. Reduced streamflow and lack of summer base flow due to diversions can
affect riparian stand recruitment and evolution. Beneficial riparian species like willow, alder and maple
require wetter riparian conditions. Dryer riparian soils promote non-native species like Eucalyptus and
various conifer species, which offer lower habitat value.
Invasive non-native species are present in all 7 tributaries of Lower Pilarcitos, frequently occurring with
high percent cover. Blue gum eucalyptus and Cape ivy appear to be the most pervasive and cover the
greatest surface area. The most highly invaded areas appear to be along lower Nuff Creek near the
confluence with Pilarcitos Creek, Mills Creek, and the lower reaches of Pilarcitos Creek. Among the 5
special-status plant species known to occur in riparian habitats within the vicinity of the watershed, only
Hickman's cinquefoil (Potentilla hickmanii), western leatherwood, and fragrant fritillary have been
reconfirmed in recent years. Section 5 provides further information regarding riparian and other plant
communities occurring in the Pilarcitos watershed.
2.4 WILDLIFE HABITAT
Section 6 describes habitat conditions for special-status wildlife species within the Pilarcitos watershed.
Species of interest include steelhead (Oncorhynchus mykiss), San Francisco garter snake, California red-
legged frog, western pond turtle, riparian-associated bird species, and marbled murrelet.
Steelhead habitat requirements change as they go through different life phases. Adult steelhead require
their natal streams to be free of barriers to migration, as the majority of spawning occurs in the upper
reaches of tributaries. Adults also need access to spawning gravel in areas free of heavy sedimentation
with adequate flow of cool, clear water. For steelhead eggs and pre-emergent fry, the most important
consideration in terms of habitat is cool water with adequate dissolved oxygen, free of fine sediment.
Cover structures such as boulder clusters and root wads provide both summer and winter rearing habit. As
juvenile steelhead grow, pools become an important habitat component.
Significant factors limiting steelhead habitat in the Pilarcitos watershed include reduced stream flow due
to flow diversions, barriers to fish passage, lack of spawning habitat (due in part to the presence of fine
sediments), and lack of rearing habitat. Habitat conditions in the Pilarcitos stream system are summarized
by reach within Section 6. Other sections describe habitat conditions and abundance for the other special
status species.

12/28/07 4
2.5 IMPLEMENTATION STATUS AND PROGRESS SUMMARY
Section 7 summarizes the implementation status of recommendations provided in the 1996 Restoration
Plan. The recommendations are summarized in a table which lists the current status of each
recommendation and provides a brief summary of actions. Recommendations which applied to the whole
watershed are listed first, and the remainder of the table is organized by sub-watershed. A brief
description of each of the ongoing and completed alternatives follows the table.

12/28/07 5
3. HYDROLOGY
The Pilarcitos Creek watershed encompasses 28 square miles in the steep coastal hills above the City of
Half Moon Bay, CA in San Mateo County (Figure 1). Pilarcitos Creek originates on the east side of
Montara Mountain and is divided by seven subwatersheds containing the following smaller tributaries:
Nuff Creek, Corinda Los Trancos Creek, Apanolio Creek, Albert Canyon, Madonna Creek, Mills Creek,
and Arroyo Leon. For the purposes of this review, Pilarcitos Creek is divided into three broad reaches:
Upper Pilarcitos, above the confluence with Albert Canyon; Middle Pilarcitos, primarily confined to an
agricultural and residential floodplain valley upstream of the confluence of Arroyo Leon; and Lower
Pilarcitos, which flows through the City of Half Moon Bay to the Pacific Coast (Figure 1).
Table 1. Pilarcitos Creek Subwatershed Characteristics

Weighted
Mean
Drainage Annual
Area Drainage Precipitation
Name (mi2) Relief (ft) (in)
Upper Pilarcitos Creek 9.1 1737 35.6
Mills Creek 3.9 1646 32.8
Upper Arroyo Leon 2.6 1844 33.5
Middle Pilarcitos Creek 2.2 916 30.9
Apanolio Creek 2.0 1649 33.4
Lower Arroyo Leon 2.0 839 28.1
Madonna Creek 1.7 1132 31.4
Lower Pilarcitos Creek 1.3 436 27.5
Albert Canyon 1.2 1175 32.8
Nuff Creek 1.1 1422 33.0
Corinda Los Trancos Creek 0.9 1627 32.4
* Weighted mean precipitation derived from the intersection of PRISM precipitation and subwatershed polygons in GIS
model.
The Pilarcitos watershed rises steeply from the outlet at Half Moon Bay at sea level into the Santa Cruz
mountains reaching a maximum drainage relief (difference between the highest and lowest elevation) of
approximately 2,044 feet near Montara Mountain. Precipitation is influenced heavily by the change in
elevation and associated change in temperature and barometric pressure (Table 1 and Figure 2). Recorded
precipitation values range from a low of 13.1 inches per year to a high of 65.5 inches per year. Mean
annual precipitation increases from 29 inches in Lower Pilarcitos to 41 inches in Upper Pilarcitos, based
on PRISM data that covers a period of approximately 30 years (1961-1990). While Upper Pilarcitos
receives more precipitation annually, Pilarcitos Reservoir and Stone Dam capture much of the water
converted to runoff. The Upper Arroyo Leon and Mills Creek subwatersheds receive slightly higher
preciptiation than the remaining subwatersheds, but the range in precipitation is also higher in these two

12/28/07 6
subwatersheds. A majority of the subwatersheds receive a mean annual precipitation of approximately 33
inches or more each year (Table 1 and Figure 2).
The hydrologic conditions are highly variable within the watershed, and subject to considerable
modification from flow diversions for both local and regional purposes. Pilarcitos Reservoir and Stone
Dam (built circa 1900) have modified flow dramatically, eliminating all of the summer flows from the
upper watershed in most years. In 2007, experimental flow releases below Stone Dam have resulting in
flow increases of 260% relative to the 1997-2006 period. Agricultural use in the watershed spiked after
World War 2, but farming and total lands under irrigation have declined in recent years (Hank Sciaroni,
pers. comm.). Hydrologic modification of tributaries (e.g. Corinda de las Trancas) has also modified
surface flows in the lower watershed. The following sections evaluate the existing hydrologic data and
information available for the watershed.
3.1 DATA SOURCES & METHODS
Streamflow data for Pilarcitos Creek was obtained from United States Geological Survey (USGS) gage
stations located near Half Moon Bay and below Stone Dam. The Half Moon Bay gage (11162630) has
operated continuously from July 1, 1966 to the present. The Stone Dam gage (11162620) has operated
from October 1, 1997 through present. Data from these stations were compiled by SWC and PWA and are
discussed in Section 3.2 Instream Flows. Streamflow measurements for several tributaries have also been
developed for various studies (e.g., Balance 2001, 2003a, 2003b).
Table 2. Available Data for USGS Gages in the Pilarcitos Watershed

Average Annual
Station Runoff
Number Station Name Available Data (acre-feet)
11162630 Pilarcitos Creek at Half Daily streamflow values for
Moon Bay 07/1/66 - 9/30/05
Unpublished streamflow data for 11,430
10/1/05 - 6/20/07
11162620 Pilarcitos Creek below Daily streamflow values for
Stone Dam, near 10/1/97 - 9/30/05
Hillsborough Unpublished streamflow data for 1,540
10/1/05 - 6/20/07
11162618 Pilarcitos Lake near Water stage values for 9/16/99 -
Hillsborough 9/30/05
Unpublished stage values for
10/1/05 - 6/20/07
Rainfall records for the upper watershed were provided by SFPUC, and represent daily rainfall totals for a
precipitation gage located on the Pilarcitos Dam. Rainfall records for the lower watershed were obtained

12/28/07 7
from the Western Regional Climate Center archive for the Half Moon Bay National Weather Service
Station (NCDC 043714-4). Annual rainfall statistics for each station are presented in Figure 3 and Figure
4 and summarized in Table 3.
Table 3. Annual Rainfall Statistics for Pilarcitos Dam and Half Moon Bay Weather Stations
Annual Precipitation (in)
Pilarcitos Dam Half Moon Bay
Min 18.4 13.1
25th% 30.1 19.3
Median 36.4 24.8
75th% 46.1 30.9
Max 65.5 55.0
Monthly precipitation values for Half Moon Bay indicate that peak precipitation usually occurs in
January, and usually ranges from nearly 3 inches/month to nearly 8 inches/month (Figure 5). Precipitation
from May through September is typically less than 0.4 inches/month. By contrast, the gage at Pilarcitos
Dam indicates that maximum daily precipitation values there often exceed 3 inches/day and can exceed 6
inches/day (Figure 6).
3.2 INSTREAM FLOWS
The following sections evaluate available instream flow information for the gaging stations at Half Moon
Bay, Below Stone Dam, and tributary subwatersheds.
3.2.1 Pilarcitos at Half Moon Bay
The average daily discharge values for Pilarcitos Creek at Half Moon Bay provide a 43-year record of
flows (Figure 7). Total annual flow patterns show an influence of climatic variability consistent with
regional patterns (Figure 8). Such patterns include drought periods (e.g. 1975-1977), extreme events (e.g.
1982), and continuous wet periods (e.g. 1994-2000). Such patterns are often cyclical, and are often
influenced by off-shore oceanic cycling (e.g. El-Nino Southern Oscillation and the Pacific Decadal
Oscillation).
Annually, flows follow a regular pattern consistent with Mediterranean rainfall-dominated runoff patterns
(Figure 9). The median annual hydrograph typically peaks in February and March near 20 cubic feet per
second (cfs). Flows are typically below 2 cfs from June through mid-November. The rising and falling
limbs of the annual hydrograph typically take 40-60 days each.
Peak instantaneous values for the Half Moon Bay gage demonstrate a very wide range of peak flow
variability (Figure 10). Several storm events produce peak flows below 500 cfs, while extreme events
(e.g. 1982) may produce over 4,500 cfs. A flood frequency analysis using a Log Pearson III method (U.S.

12/28/07 8
Interagency Advisory Committee on Water Data, 1982) suggests a 50% probability of a peak flow equal
to 700 cfs or more and a 1% probability of a peak flow of 3,800 cfs or more in any given year (Figure 11).
Historically, baseflow1 discharge at Half Moon Bay has been very low (Figure 12). Until about 1998,
summer flow would often be zero for several weeks at a time. Since 1998, some level of average daily
flow has been maintained in all but a single day, usually exceeding 0.5 cfs. However, this period has been
relatively wet when compared to the historical record (Figure 8).
The USGS has rated the stream gage at Half Moon Bay as “fair,” which implies that the hydraulic control
at the stream gage location is somewhat dynamic. The rating curve for peak discharges (Figure 13)
indicates that similar discharges occur over a 2-3 foot range in the gage height over time. Since the rating
curves are continually updated by the USGS, the effect on the discharge record is somewhat constrained.
However, the record of the shifts in the rating curve can be used to explore the pattern of channel change
at the gage location. Such changes can be attributed to deposition, channel widening, channel deepening,
or vegetative growth/removal. Figure 14 shows several cycles of change that appear to be consistent with
translation of sediment deposits through the site.
3.2.2 Pilarcitos at Stone Dam
The average daily discharge values for Pilarcitos Creek below Stone Dam provide a nearly 10-year record
of flows (Figure 15). Flow patterns show a strongly reduced flow and truncated hydrograph relative to the
contributing basin area, driven primarily by a few weeks of peak runoff each year. Most runoff is retained
by Pilarcitos Reservoir.
The annual hydrograph below Stone Dam clearly shows the effects of water supply regulation (Figure
16). Winter flows rarely exceed 5 cfs and typically do so only during extreme flow years. The duration of
peak flows is short, usually only a few weeks each year. The majority of flows below Stone Dam are well
below 1 cfs. However, since the channel is relatively small here (Table 4), a discharge of 1 cfs is
equivalent to a flow depth of about 0.31 feet (Figure 17).
Table 4. Typical Wetted Channel Dimensions During Site Discharge Measurements

Wetted Wetted Average Mean Gage
Discharge Channel Channel Wetted Velocity Height
USGS Gage Site (cfs) Width (ft) Area (ft2) Depth (ft) (ft/s) (ft)
Below Stone Dam Station 0.39 2.5 0.82 0.38 0.55 4.83
Half Moon Bay Station 4.50 9.5 3.81 0.41 1.42 2.72
The USGS has rated the stream gage below Stone Dam as “poor,” which implies that the hydraulic
control at the stream gage location is significantly dynamic. This may be in part due to the very low
1
Baseflow refers to the dry season flow not associated with any particular storm, but representative of the “base” of
the hydrograph.

12/28/07 9
quantity of discharge and the relatively small channel that can dramatically limit the accuracy of
streamflow measurements. The existing rating curve for peak discharges (Figure 17) indicates that flows
rarely exceed a stage of 2 feet. Observed shifts in the rating curve (Figure 17) suggest chronic aggradation
prior to December 2002 when a significant channel change occurred (most likely a large deposit of
sediment or debris). Based on the rating curve, the channel appears to have naturally recovered from this
disturbance by October 2004 and has been relatively stable since.
The summer of 2007 has been an unusual period for Pilarcitos Creek. While most other Central Coast
streams reflected low water years (based on USGS exceedance records), Pilarcitos experienced a high
water year, on most days exceeding 90% of the historical flows for any given day. A period of
“experimental” flow releases below Stone Dam occurred in the summer of 2007, and these flows appear
to be at least partially responsible for the higer-than-normal flows in the lower watershed. Despite the
modest quantity of water released at Stone Dam in 2007, the proportion of flows from the upper
watershed increased by 37% from May through September.
Table 5. Average monthly flow conditions for Pilarcitos Creek

2007 Average Proportion of Flows
Monthly Discharge from Above Stone
(cfs) Dam
Stone HMB 1997-2006
Dam 2007 Average
Oct 1.65 2.69 57% 14%
Nov 2.70 5.22 64% 8%
Dec 2.07 6.74 44% 7%
Jan 1.12 5.52 19% 11%
Feb 4.05 29.52 13% 10%
Mar 6.58 17.63 25% 8%
Apr 1.55 6.81 24% 8%
May 1.67 4.11 39% 9%
Jun 1.51 3.40 46% 11%
Jul 1.25 1.95 65% 14%
Aug 0.63 1.39 50% 16%
Sep 0.55 1.14 53% 18%
3.2.3 Contribution from Tributary Streams
The watershed below Stone Dam is a significant contributor to flows in Pilarcitos Creek at Half Moon
Bay (Figure 18, Figure 19, and Figure 20). Anecdotal reports suggest that Apanolio and Arroyo Leon also
contribute significant flows to the lower watershed, though the former subwatershed is not large relative
to the other subwatersheds.

12/28/07 10
While existing gage records are limited for the subwatersheds, stream gages were installed in two
tributaries as reported in Balance (2001). Summary hydrologic statistics are provided for 1-3 years of data
when instream gages were operational. These studies were developed to address specific land-use issues
and opportunities, and did not seek to compare streamflow conditions in these watersheds against those in
other subwatersheds within the Pilarcitos watershed.
While acknowledging the limitations of these data sources, we developed an estimate of the relative
contribution of annual flow from each of the subwatersheds (Table 6). Adjusted annual flows do not
distinguish between peak runoff and baseflow runoff periods, and therefore extrapolation to other
hydrologic evaluations must be considered carefully. For example, Pilarcitos Creek below Stone Dam
(Pilarcitos at Sare, located a short distance downstream from where Highway 92 crosses Pilarcitos Creek)
contributes over 33% of the total annual flow for the watershed. However, most of this flow occurs during
peak runoff periods when Pilarcitos Reservoir and Stone Dam are releasing flows. During low-flow
periods, the contribution from this reach is much less. By contrast, Apanolio Creek has been observed to
offer flows during low-flow periods, when its relative contribution to baseflows probably exceeds 12%.
In general, flows in Middle and Lower Pilarcitos Creek are predominantly provided by the subwatersheds
of Middle Pilarcitos, Arroyo Leon, and Apanolio. This preliminary analysis does not consider the
influence of groundwater exchange or local diversions.

12/28/07 11
Table 6. Estimated Annual Water Budget
Unit Mean Flow * (cfs/mi2) Total Adjusted Annual Flow (ac-ft/yr) **
Functional Total Subwatershed
Drainage Area Area
(sq mi) (sq mi) 1998 1999 2000 1998 1999 2000
Upper Arroyo
Leon 2.6 2.58 2.42 1.0 0.92 4,531 12% 1,872 10% 1,723 11%
Mills Ck at
Higgins Road 3.82 3.81 2.23 0.94 0.84 6,163 17% 2,598 14% 2,321 15%
Lower Arroyo
Leon 2.15 2.33 0.97 0.88 3,621 10% 1,511 8% 1,371 9%
Pilarcitos Ck at
Sare 3.9 3.9 3.97 2.23 1.91 11,217 30% 6,301 35% 5,397 36%
Madonna Ck at
POST 1.13 1.68 1.94 0.78 n/a 2,356 6% 947 5% n/a
Apanolio Ck 1.12 2.05 2.57 1.67 1.21 3,824 10% 2,485 14% 1,800 12%
Corinda Los
Trancas 0.39 2.57 1.67 1.21 726 2% 472 3% 342 2%
Nuff Ck 0.88 2.57 1.67 1.21 1,638 4% 1,065 6% 771 5%
Middle
Pilarcitos Ck 3.93 2.57 1.67 1.21 7,317 20% 4,755 26% 3,445 23%
Pilarcitos Ck at
Hwy 1 20.77 20.77 2.45 1.20 1.01 36,865 100% 18,057 100% 15,198 100%
* Italicized data inferred from monitored sites. **Italicized data adjusted to remove upstream subwatersheds already included in budget
Note: Unit Mean Flow and Drainage Area from Balance Hydrologics (2003a). All percentages relative to Pilarcitos Creek at Hwy 1. Budget does
not account for flow diversions or net loss (gain) to groundwater.
P:\Projects\1884_Pilarcitos_IWMP\Task4_IWMP\reports\1884-00_Wshed_Assess_Update\Pilarcitos Creek IWMP Watershed Assessment Update.doc

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3.2.4 Hydrologic Effect of Eucalyptus Globulus
The presence of Eucalyptus globulus (blue gum eucalyptus) in the Pilarcitos Watershed is thought to be a
potential factor affecting streamflows and hydrologic processes. (See also Section 5, Riparian Ecology,
for a discussion of the prevalence of this tree species in the watershed and its role in the condition of
riparian habitat.) The basis for this hypothesis is described below.
E. globulus shows high rates of evapotranspiration, even in low water conditions (Pryor 1976). Many
drought-tolerant plants have developed methods to slow their water losses but the blue gum appears to
have taken a different strategy by developing an extensive root system capable of extracting water from
great depths (Bell and Williams 1997). In addition to deep roots, eucalyptus trees can extract water at
higher tension levels than some other plants (Pryor 1976), which means they can out-compete plants with
inferior water extraction capabilities. Eucalyptus water consumption exceeds that of “ecologically
comparable evergreen California chaparral species” (Bell and Williams 1997). In studying whether
growing E. globulus commercially would impact a municipal water supply, researchers in South Africa
found that, not only did eucalyptus trees reduce available surface water, they completely eliminated any
evidence of flow in what was once a perennial stream (Scott and Lesch 1997).
In addition to groundwater extraction, E. globulus has been associated with high levels of soil
hydrophobicity. Soil hydrophobicity, also referred to as soil water repellency, is the condition where soil
resists wetting; water applied to the soil surface either runs off or remains on the surface rather than
infiltrating the soil (Doerr 1998, Ferriera et al. 2000, Shakesby et al. 2000). Areas of eucalyptus forest in
the Mediterranean climates of Portugal exhibited some of the highest levels of soil water repellency ever
measured (Leighton-Boyce et al. 2005). Soil under E. globulus has shown greatly elevated hydrophobicity
when compared to soil under nearby Quercus agrifolia (coast live oak) in coastal California hillslopes
(Thompson 2006). Environmental impacts of elevated hydrophobicity include increased flood risk,
enhanced “preferential flow and associated leaching of nutrients and agrochemicals,” reduced microbial
activity, and reduced seed germination and crop growth (Doerr et al. 2005).
Shakesby et al. (2000) observed several effects of elevated soil hydrophobicity at small scales and in lab
experiments, associating it with reduced aggregate stability, reduced infiltration, enhanced overland flow,
increased rainsplash-induced detachment of soil particles, and increased soil erosion. Greater splash
detachment is associated with more erosion (Shakesby et al. 2000).
3.3 REVIEW OF WATER SUPPLY RESOURCES
Water in the Pilarcitos Creek watershed is used by the SFPUC, the CCWD, the Ocean Colony Golf
Course, and local agricultural and domestic users. Figure 21 shows the Pilarcitos Creek Water Supply
System currently used by the SFPUC and CCWD, which diverts water from the upper portion of
Pilarcitos Creek at Pilarcitos Dam and Stone Dam.
The state of water supply diversions for the Pilarcitos watershed is complex and our understanding is still
evolving. There are several remaining data gaps associated with specific water supply diversions. In some

12/28/07 13
cases, data may be available, but are not available in easily useable formats. In other cases, specific water
supply usage data has not been historically collected (e.g. private residential uses, etc.). The following
sections summarize our current understanding.
3.3.1 San Francisco Public Utilities Commission
The San Francisco Public Utilities Commission (SFPUC) operates reservoir facilities in the upper
Pilarcitos watershed. The facilities include Pilarcitos Reservoir, Stone Dam, water conveyance pipelines
and tunnels, various buildings and roads. The SFPUC owns the land comprising the upper watershed of
Pilarcitos Creek and the stream corridor from Stone Dam Reservoir extending downstream approximately
1 mile. SFPUC controls access to these lands to protect water quality, and has managed the upper
watershed for a number of environmental benefits. EOA (1990) indicated that SFPUC diversions capture
28 percent of the total watershed runoff, the largest amount among existing water users.
.Pilarcitos Reservoir has a catchment area of 3.8 square miles (about 2400 acres) and storage capacity of
approximately 3,100 acre-feet (1,010 million gallons [MG]). Approximately half of this capacity is
maintained as emergency storage for the SFPUC system (pers. comm.). Approximately 1,150 acre-feet of
water is available for gravity release to Pilarcitos Creek.
Stone Dam Reservoir is located approximately 2.3 miles downstream of Pilarcitos Reservoir.
Kennedy/Jenks (2006) indicates that it has a capacity of approximately 14.5 acre-feet (5 MG). However it
is unclear whether that capacity is currently available or some percentage is lost due to sedimentation in
the reservoir. Stone Dam Reservoir captures and directs water either to CCWD via Lower Crystal Springs
Reservoir (Kennedy/Jenks 2006).
Pilarcitos Reservoir is supplied by runoff, primarily during the rainy season. Pilarcitos Reservoir storage
is used to supply water transfers to the SFPUC’s Reservoir system in the San Mateo Creek watershed
(San Andreas and Crystal Springs Reservoirs) and for use by CCWD. Water is diverted into San Andreas
Reservoir via a conveyance tunnel from Pilarcitos Reservoir and to Lower Crystal Springs reservoir via a
conveyance tunnel diversion at Stone Dam. Most of the water in the San Andreas and Crystal Springs
reservoirs comes from the Hetch Hetchy water system. Water deliveries to CCWD are provided directly
from Pilarcitos Reservoir through Pilarcitos Creek via diversions operated by CCWD at Stone Dam.
Excess capacity is transferred from Pilarcitos Reservoir to San Andreas Reservoir and from Stone Dam to
Crystal Springs Reservoir. Flows exceeding the capacity of Pilarcitos Reservoir and the capacity for
deliveries are spilled over Stone Dam, providing instream flows to Pilarcitos Creek. Until recently,
releases from Stone Dam to Pilarcitos Creek were limited to these brief periods of excess capacity, and
stream flow immediately below the dam consisted only of leakage through the spillway boards and
seepage through the dam. In 2007, experimental releases were made as part of a study of aquatic
resources. These releases have resulted in average streamflow below Stone Dam between June and
September 2007 of 1.96 cubic feet per second (cfs).

12/28/07 14
3.3.2 Coastside County Water District
The Coastside County Water District (CCWD) serves the City of Half Moon Bay and a part of the
unincorporated area of San Mateo County including Miramar, Princeton By The Sea and El Granada. The
District's service territory encompasses approximately 14 square miles and serves nearly 18,000 people.
CCWD has three water supply sources that affect Pilarcitos watershed; Pilarcitos Lake or Reservoir,
Crystal Springs Reservoir, and the Pilarcitos Well Field. Supplies from Pilarcitos and Crystal Springs
Reservoirs are provided by SFPUC. CCWD also operates a supply reservoir outside the Pilarcitos
watershed. The entire system consists of two water treatment plants, 17 miles of transmission pipeline, 83
miles of distribution pipeline, several water storage tanks, and other equipment. The average annual yield
from these four sources is about 2800 ac-ft. Approximately 1,800 ac-ft of water is supplied from the
SFPUC sources and the remaining water is supplied locally.
The area in Upper Pilarcitos downstream of SFPUC property to the confluence with Albert Canyon is
controlled by CCWD. Approximately 75 percent of CCWD’s water supply comes from SFPUC. CCWD
currently derives approximately 40 to 45 percent of its annual water supply from two water supply
sources in the Pilarcitos watershed: Pilarcitos Reservoir and several well fields. CCWD purchases water
from SFPUC under an agreement executed in 1984. CCWD is currently entitled to purchase a minimum
of approximately 2,446 acre-feet (800 MG) per year (combined from Pilarcitos Reservoir and Upper
Crystal Springs Reservoir) except in drought years (CCWD 2006). The yield of Pilarcitos Reservoir was
estimated to be 1,590 acre-feet (520 MG) per year (CCWD 2006). The agreement between CCWD and
SFPUC expires in 2009, at which time a new contract will be negotiated and implemented. The Pilarcitos
Reservoir supply source is important to the CCWD because of high dependability and the low operating
cost as a result of the flow by gravity.
Water delivered to CCWD from SFPUC is supplied either by gravity flow from Pilarcitos Reservoir or is
pumped from Crystal Springs Reservoir. Pilarcitos Reservoir produces up to 7.7 acre-feet per day by
gravity flow. When the daily demand exceeds the available supply from Pilarcitos Reservoir, water is
supplied from the Crystal Springs Reservoir Pump Station. Water in Crystal Springs Reservoir comes
from excess flows captured from Pilarcitos Creek as well as the Hetch Hetchy supply in Little Yosemite
Valley in the Sierras. The Crystal Springs Water Supply project was completed in 1994 and consists of an
eight-mile pipeline connected to a pump station and intake tunnel under the reservoir terminating at the
Nunes Water Treatment Plant. Deliveries taken from Crystal Springs Reservoir and Pilarcitos Reservoir
are limited by the capacity of the Nunes Plant, currently 4.5 MG per day or 13.8 acre-feet per day.
In addition to the reservoirs, the CCWD obtains water from a group of 7 wells located downstream of
Stone Dam reservoir, approximately 4,500 feet to 7,300 feet north of Highway 92 in Pilarcitos Creek
Canyon. The CCWD well field is operated under a permit from the State Water Resources Control Board
(SWRCB), which limits annual extraction to 360 acre-feet (117 MG), and limits pumping to the winter

12/28/07 15
wet season period from November 1 to March 31, thereby prohibiting operation April to October. The
maximum permitted extraction rate is 1.5 cfs (674 gallons per minute), and the reported operational
pumping capacity is reportedly similar. Balance (1997) estimates an operational capacity of 2.0 cfs,
including the new more efficient well 4A (see Section 2.2.4.1 for more information on CCWD well
operations). CCWD operates the well field within the permit conditions and with the additional constraint
of a CCWD management philosophy that well field operations should not result in a dry creek
(Kennedy/Jenks, 2006). Therefore, the total amount of water that the CCWD can obtain from the
Pilarcitos watershed is approximately 1,950 acre feet.
The District maintains a distribution system that includes three pressure zones, five pump stations, 500
hydrants, and 52 miles of water mains and 100 miles of transmission and distribution pipeline. This
infrastructure also includes ten treated water storage tanks in the system, which have a combined storage
capacity of 8.1 MG or 24.9 acre-feet.
3.3.3 Other Water Rights
We updated the previous summary of permitted and unpermitted water rights diversions using SWRCB
WRIMS database (http://www.waterrights.ca.gov/ accessed on June 20, 2007). Figure 22 is a map of
diversions as registered at the WRIMS database from the Restoration Plan (PWA, 1996) and from 2007.
Table 7 summarizes permitted appropriative water rights diversions, as well as statements of pre-1914
diversions for each subwatershed. The amount of permitted appropriative diversions in the watershed total
about 878 acre-feet per year. Most appropriative users are prohibited by conditions in their permit or
licenses from diverting water during the summer. The amount of riparian diversion and pre-1914
appropriative diversions are reported in statements filed with the SWRCB as 2,296 acre-feet per year. The
details of both permitted diversions and statements are provided in Table 7.
The total amount of water available to be diverted from the streams amounts to 3,174 acre-feet per year.
However, actual usage varies considerably. Not all water rights can be exercised every year. In addition,
some water rights uses are consumptive (e.g. water is completely removed from the system), while other
uses are less consumptive. For example, agricultural uses may include irrigation practices that return
some water to the stream via return flow or infiltration to local floodplain aquifers. As a result, accurate
water budgets for the basin are difficult to develop.

12/28/07 16
Table 7. Summary of Permitted Appropriative Diversions and Statement of pre-1914 Diversions
Permitted Appropriative Statement of pre-1914
Water Rights Diversions Water Diversions
Creek (acre-feet) (acre-feet)
Pilarcitos Creek 528 1,426
Arroyo Leon 107 30
Apanalio Creek 75 667
Nuff Creek 96 106
Albert Canyon 72 66
TOTAL 878 2,296
3.4 GROUNDWATER RESOURCES
The groundwater setting of the Pilarcitos watershed is characterized by two aquifers. The first is a coastal
plain aquifer (the Lower Pilarcitos Creek Groundwater Basin) which is located generally beneath the
town of Half Moon Bay (Kennedy/Jenks, 2006). This aquifer is composed of shallow, unconfined and
semi-confined, unconsolidated terrace deposits and alluvial sediments. This aquifer is thin, usually with
less than 40 feet of saturated thickness, and is underlain by Purisima Sandstone bedrock at 40-80 feet.
The second aquifer is a narrow mountain valley system formed by Pilarcitos Creek and its tributaries.
This alluvial aquifer is bounded by a variable depth, low-permeability bedrock channel with shallow
alluvial aquifers comprised of loose unconsolidated sand and gravels. It is discontinuous, limited in area,
and has high transmissivities in some existing wells (such as the CCWD Pilarcitos Canyon well field). It
is likely to be in direct hydrologic connection with the Pilarcitos surface water, so pumping can affect
streamflows and may not draw directly on water stored in the aquifer.
3.4.1 Upper Pilarcitos
In the Upper Pilarcitos Creek Watershed (above the confluence with Albert Canyon), available
groundwater appears to be stored in alluvial deposits in a narrow bedrock channel following the surface
flow, bounded by low permeability bedrock. Six of the seven CCWD wells in Upper Pilarcitos are older,
low-efficiency wells drilled prior to 1970. The exception is one recent, more efficient and high-yielding
well, 4A, completed in 1995. All seven wells are completed and screened in the shallow alluvium, with
total depths of less than 50 feet, and water levels at less than 10 feet deep (Balance 1997).
These wells are in direct connection with stream flow, and reportedly have the ability to dry up the stream
when pumped during periods of low stream flow (Kennedy/Jenks 2006). During a 1995 test pumping of
new well 4A, pumping at a rate of 265 gallons per minute (gpm) reduced flow in Pilarcitos Creek from
approximately 200 gpm to about 20 gpm (Balance 1997). This indicates that the Pilarcitos Canyon well
field and the Pilarcitos Creek flow are directly linked, and surface flow can be effectively captured by
pumping from the alluvial aquifer. This pumping test also indicated a high transmissivity for this alluvial

12/28/07 17
aquifer, meaning that the operational pumping limits of the existing well field (total pumping rate of 1.5
cfs) are due to limits from the existing well design and construction, not limits of the aquifer. Two recent
reports (Balance 1997, Kennedy/Jenks 2006) have reviewed the operation of Pilarcitos Reservoir, Stone
Dam Reservoir, and the Pilarcitos Canyon well field to evaluate options to improve aquatic habitat,
including increasing the stream flows in a portion of Pilarcitos Creek below Stone Dam and recapturing
the water at the Pilarcitos Canyon well field.
3.4.2 Middle Pilarcitos
In the middle section of the Pilarcitos Creek watershed (defined here to include the confluence with
Arroyo Leon), available groundwater is limited to alluvial deposits in a narrow bedrock channel following
the surface flow, bounded by low permeability bedrock. There are a number of poorly documented
surface diversions and private groundwater wells in alluvium for agricultural and domestic use, but no
municipal groundwater production. Water extraction by both surface diversions and groundwater
pumping from alluvial wells in connection with surface flow is believed to limit and reduce dry season
flow in Pilarcitos Creek. (Balance 1997).
3.4.3 Lower Pilarcitos
Below the confluence with Arroyo Leon, Pilarcitos Creek emerges from the mountain valley drainage
system onto the coastal plain, and flows through the town of Half Moon Bay and into the Pacific Ocean.
This area is underlain by the Lower Pilarcitos Creek Groundwater Basin, which is composed of shallow,
unconfined and semi-confined, unconsolidated terrace deposits and alluvial sediments (Todd Engineers
2003). This aquifer has less than 40 feet of saturated thickness and is underlain by Purisima Sandstone
bedrock at 40-80 feet. Groundwater elevations fluctuate by 10-20 feet seasonally, which is a dramatic
change in an aquifer with potentially only 30 feet of saturated thickness in some areas. Because of the
proximity and connection to the Pacific Ocean, this aquifer is vulnerable to sea water intrusion from
overpumping. No sea water intrusion has been identified.
Many wells have been drilled in this portion of the watershed over time, but many wells have been
abandoned due to changes in land use, and to availability of municipal water from the CCWD. The most
important groundwater pumping in this basin is the Ocean Colony Partners Balboa well field, used for
irrigation of 2 golf courses. Todd Engineers (2003) estimates total pumping in this basin for export or
consumption of 510 acre-feet per year in 2003.
The Lower Pilarcitos Creek aquifer is no longer being used as a source of drinking water. In 1997, five
test wells were installed and pumped by the CCWD to evaluate potential for increased groundwater
production from the Lower Pilarcitos Creek Groundwater Basin (Nelson 1997, 1998). These wells have
been (or are in the process of being) decommissioned by CCWD for a number of reasons. These wells
had promising yields, and CCWD hired Todd Engineers to complete a water balance for the aquifer and
to estimate a sustainable pumping yield. Todd Engineers (2003) estimated a total remaining sustainable

12/28/07 18
annual pumping of 1,300 acre-feet per year from this aquifer (based on 60% of estimated outflow to
Pacific Ocean) and suggested a total average annual yield from the proposed 5-well Lower Pilarcitos well
field of 595 acre-feet per year. This pumping was proposed to be seasonal to avoid creating seawater
intrusion and was intended to capture groundwater outflow to the ocean from the aquifer, not reduce
existing streamflows in Pilarcitos Creek. Todd Engineers (2003) also recommended blending
groundwater with Crystal Springs water to reduce dissolved minerals, and conducting stream flow
monitoring in the lower reaches of Pilarcitos Creek to assess the potential for inducing groundwater
recharge to the aquifer from the creek by pumping. An engineering evaluation of this proposed well field
for CCWD found that the cost of water from the proposed Pilarcitos Creek well field was expected to be
similar to the cost of water from Crystal Springs Reservoir (Teter 2002).
3.5 WATER QUALITY
EOA (1990) commented on the lack of available water quality data for the Pilarcitos watershed. We will
work with stakeholders to gather more data and, wherever necessary, to fill this data gap as we develop
the IWMP.
The EOA report (1990) references an assessment of water quality adopted by the RWQCB which rates
Pilarcitos Creek and Pilarcitos Lake with a Resource Value of 1 (outstanding water bodies). In the
Corinda Los Trancos Creek tributary, there is extensive groundwater monitoring and surface water quality
data associated with operation of the Ox Mountain Sanitary Landfill by Browning-Ferris Industries (BFI),
a trademark of Allied Waste. This monitoring data (RWQCB 2006) suggests landfill impacts to
groundwater are limited to the area beneath the landfill, and surface water impacts are limited to elevated
bacteria levels in Corinda Los Trancos Creek (perhaps due to the landfill’s seagull population). A leachate
collection and disposal system is operated at the downstream end of the landfill.
Heal The Bay’s (HTB) 14th Annual Beach Report Card (2004) assigned the lowest rating for water
quality (F) to Venice Beach for both dry and wet weather conditions, based on the County of San Mateo’s
AB411 regulatory weekly water quality sampling. HTB reports that the County of San Mateo (County)
completed an upstream source identification-monitoring program to determine potential sources of fecal
bacteria in Frenchman’s and Pilarcitos Creek. The County located and abated a point source along
Frenchman’s Creek, where a landowner was storing a large amount of manure adjacent to a storm drain
which drained directly to Pilarcitos Creek. However, the most recent HTB Annual Beach Report Card
(2007) reports that Venice Beach still has poor water quality in dry and wet weather conditions. No
subsequent monitoring data or reports were available.
3.5.1 Water Treatment Facilities
The Sewer Authority Mid-Coast (SAM) owns and operates a water treatment plant located at Half Moon
Bay. The plant provides secondary level treatment for domestic and industrial wastewater from the City
of Half Moon Bay, Montara Sanitary District, and Granada Sanitary District. SAM’s service area has a

12/28/07 19
present population of 20,000. The treatment plant has an average dry weather flow design of 2.0 MG per
day (mgd), and can treat up to 2.5 mgd during the wet weather flow period. The plant presently
discharges an average dry weather flow of 1.5 mgd, and an annual average effluent flow of 1.525 mgd.
Treated wastewater is currently discharged into the Pacific Ocean within the Monterey Bay National
Marine Sanctuary, an area of special biological significance. The discharge point is west of Pilarcitos
Creek through a submerged diffuser about 1900 feet offshore at a depth of 37 feet below mean lower low
water. Water is discharged with an initial dilution ratio of 119:1.

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4. GEOMORPHIC CONDITIONS
Stream channel geomorphology is determined by the runoff and sediment characteristics of a watershed.
In a stable stream channel, runoff and sediment are in balance and the channel neither erodes nor aggrades
over time though channel will adjust dynamically to individual runoff events. Different reaches can be
sources of sediment, transport sediment, or be sinks of sediment depending on their location in the
watershed. In general, headwater tributary channels are sediment sources as they erode into the
surrounding landscape, mid-section reaches are transportational, and downstream reaches are depositional
as their lower gradient causes sediment eroded upstream to deposit out on a floodplain. However, over
geological time, erosion, transport and deposition are in balance and the stream channel remains
dynamically stable.
When watershed runoff or sediment characteristics are altered rapidly by human activity, stream channels
are often unable to adjust quickly enough to maintain a stable configuration. Watershed development,
including grazing and other agricultural uses, can cause rapid increases in runoff frequency, intensity and
volume which in turn trigger channel erosion. Throughout the Bay Area, stream channels commonly
respond to these changes by “incising” into the landscape, so that flood flows are not able to access the
surrounding floodplain. Concentrated runoff in incised channels can scour channel beds and undermine
banks, generating increased sediment and destabilizing both channel and banks.
Streamflow regulation due to dams and/or diversions also has the potential to affect long-term channel
morphology. Reduced peak flows and shorter flow durations reduce sediment transport, causing excessive
deposition and/or channel braiding. On the other hand, dams can also reduce sediment supply by trapping
coarse sediment, causing or exacerbating channel erosion in the downstream channel.
4.1 DATA SOURCES AND METHODS
The primary data sources for our description of the geomorphic evolution of the watershed were previous
reports by Balance (2001, 2003a, 2003b) and the Restoration Plan (PWA 1996). In addition to these
reports, we reviewed the oral histories collected from local stakeholders (Appendix B), aerial photos of
the watershed, and historic USGS quadrangle maps.
As a foundation for this assessment, we compiled a spatial database of physical watershed parameters
which affect channel sedimentation and morphology (Appendix A). In addition to a road map provided by
the SFPUC (Figure 28 and Appendix A), we also acquired the following data layers for use in Geographic
Information System (GIS):
Digital Elevation Model from the USGS Seamless Data Distribution System (SDDS),
Soils from the National Resources Conservation Service SSURGO database
Geology of San Mateo County (Brabb et al. 1998) available via the USGS Open Online Geologic
Map Database

12/28/07 21
Debris flows in San Mateo County resulting from the 1982 storm (Ellen et al. 1997)
We spatially defined hydrology in the watershed using several GIS tools, including the ESRI ArcHydro
Tools extension and IDRISI’s Kilimanjaro raster analysis tools. We used these tools to classify channel
characteristics such as stream gradient and morphology, develop longitudinal profiles of mainstem
channels, develop statistics of hillslope and channel gradient by subwatershed, and develop slope hazard
maps. We also digitized features from the Restoration Plan (PWA, 1996) such as gullies, bank erosion
sites, road-related erosion sites, and landslides.
4.2 WATERSHED GEOLOGY
Geology in the Pilarcitos watershed is primarily a mixture of sedimentary and volcanic rocks (Figure 23)
(Brabb et al. 1998). Sedimentary rocks of the Franciscan assemblage and the Monterey Formation are
found throughout the eastern part of the watershed in the Madonna, Mills, and Arroyo Leon
subwatersheds and are found to a lesser degree in the Apanolio and Corinda Los Trancos subwatersheds.
Limestone and greywacke exist in Upper Pilarcitos above Pilarcitos Reservoir. Volcanic rocks,
predominantly granitic rocks of Montara Mountain (Brabb et al., 1998), are found throughout the western
part of the watershed in the Upper Pilarcitos, Apanolio, Corinda Los Trancos, and Nuff Creek
subwatersheds.
Rocks of the Franciscan assemblage vary in composition and texture, and therefore in erodibility. The
sedimentary rocks underlying the Mills Creek and Arroyo Leon subwatersheds are consolidated (Balance
2001) and generally considered fine-grained. The Monterey and Lompico formations are also fine-grained
in texture and are susceptible to erosion. The granite and granodiorite on Montara Mountain are deeply
fractured and highly weathered, transforming to coarse sand. Balance (2001) measured sediment delivery
at the base of each of five of the Pilarcitos subwatersheds (Upper Pilarcitos, Apanolio, Corinda Los
Trancos, Madonna, Mills, and Upper and Lower Arroyo Leon) and noted that the granite, due to the
softness of the minerals, crumbles easily.
The parent material (bedrock) in the Pilarcitos Watershed is reflected by the soil particle size assigned in
the SSURGO soils database compiled by the United States Department of Agriculture (USDA) (Figure
24). Soils in the Pilarcitos watershed are predominantly of mixture sand and silt with fewer soils
dominated by clay (Figure 24). Higher percentages (~63 to 96%) of sand are coincident with granitic
rocks, and moderate percentages of silt (~34 to 53%) mixed with sand are coincident with sedimentary
rocks primarily in the Mills Creek and Arroyo Leon subwatersheds (Figure 24).
4.2.1 Landslides, Debris Flows and Hillslope Erosion
In 1982, a high magnitude rainfall event occurred over a wide region of the San Francisco Bay area
including San Mateo County and the Pilarcitos watershed (Brabb et al. 1998). This event triggered
hundreds of debris flows in the Pilarcitos watershed. Such debris flows can be a significant source of

12/28/07 22
sediment depending on their proximity to the channel (Figure 23). PWA (1996) performed a watershed
reconnaissance to catalogue gullies, landslides, bank erosion sites, and road-related erosion events (Figure
23). The lack of spatial correlation between the location of 1982 debris flows and the location of gullies
and landslides catalogued in the Restoration Plan (PWA, 1996) underscores the stochastic nature of
hillslope erosion. Figure 23 also demonstrates the widespread contribution from hillslope failure to
available sediment in the Pilarcitos watershed.
The extent to which natural hillslope erosion (gullies, landslides, debris flows) contributes to channel
sedimentation is defined by the source-area gradient or slope, convergence, deposition-site conditions,
and connectivity with the Pilarcitos Creek mainstem and/or the tributary channels (Benda and Cundy
1990). This connection between the hillslope and the channel is influenced heavily by the steepness of the
slopes in the watershed. Steeper, convergent slopes also tend to be more erosive as they are more prone to
failure in the form of landslides and debris flows (Deitrich and Dunne 1978). Upon failure, such features
create a “hollow” that cyclically fills and evacuates over a period of decades to millennia (Dietrich et al
1987). The proportion of each watershed that contains these sources of landslide and debris flow sediment
was evaluated by integrating a two different DEM analysis tools (convergent channel network and slope)
and performing basic statistics for the distribution of these features. The convergence channel network
was defined for all linear features with a contributing area greater than 5 acres, and equals over 416 miles
for the entire watershed, 61% of which includes hollows (Table 8). The steep convergent channels are
predominant in the reach below Stone Dam, Nuff Creek and Apanolio Creek (Figure 26).

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Table 8. Convergent Channel Network
Convergent Channel Distribution Greater Than 60% Slope Total Length
90th Watershed Length Density Total Length Density

%ile Median Area (ac) (ft) % (ft/ac) (ft) (ft/ac)
Upper Arroyo Leon 57 31 1,654 14,828 8% 9 189,101 114
Mills Ck 54 32 2,441 17,469 6% 7 289,915 119
Lower Arroyo Leon 34 13 5,470 792 0% 0 164,992 30
Lower Pilarcitos Ck 6 2 17,949 2,302 1% 0 199,024 11
Middle Pilarcitos Ck 45 21 11,516 7,735 3% 1 264,372 23
Madonna Ck 47 25 1,073 2,566 2% 2 116,811 109
Apanolio Ck 61 38 1,314 20,412 12% 16 167,029 127
Cordina Los Trancos 54 25 561 3,962 6% 7 65,461 117
Nuff Ck 62 40 247 10,791 13% 44 80,176 325
Stone Dam Reach 116 2 1,758 32,221 16% 18 200,609 114
Regulated Reach 50 31 4,048 14,300 3% 4 461,283 114
Upper Pilarcitos Ck 56 33 5,806 46,521 7% 8 661,891 114

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We used the DEM to calculate the slopes in each sub-watershed (Figure 27). The smaller subwatersheds
in the Middle Pilarcitos region, such as Apanolio, Corinda Los Trancos, and Nuff, have a higher average
hillslope gradient (Table 8 and Figure 27). The section of Pilarcitos Creek below Stone Dam and above
Albert Canyon, Upper Arroyo Leon and Mills Creek also has a high average hillslope gradient (Table 8
and Figure 27).
These results are consistent with measurements of sediment discharge in five of the Pilarcitos
subwatersheds performed by Balance (2003a) during Water Year 2000 (October 1, 1999 – September 30,
2000). They measured sediment discharge near the downstream outlet of Mills Creek, Upper Arroyo
Leon, Corinda Los Trancos, and Apanolio Creek. They also measured sediment discharge along Pilarcitos
Creek just below the confluence with Albert Canyon and the road crossing at Highway 92. Data from
their study confirms that the primary sediment sources include Apanolio Creek and Upper Pilarcitos
Creek.
Balance (2003a) suggested that this result was counter-intuitive because of the sedimentary rocks found in
the Arroyo Leon and Mills Creek which they described as more erodible than the granitic rocks of
Montara Mountain. However, both Balance (2003b) and Brabb et al. (1998) note the highly fractured and
deeply weathered nature of the granitic rocks found in the Apanolio, Corinda Los Trancos, and Nuff
Creek subwatersheds and in the lower portion of Upper Pilarcitos below Stone Dam (Figure 23). These
subwatersheds also contain a high average hillslope gradient and a larger area with slopes greater than
60% (Figure 26 and Figure 27).
4.2.2 Land Use Impacts
One of the biggest impacts in the history of the Pilarcitos watershed was the increase in sedimentation
resulting from the failure of the diversion dam at the downstream end of the Browing-Ferris Industries
Landfill in 1992 (PWA 1996, RCD 2007b). This event in the Corinda Los Trancos watershed contributed
massive quantities of sediment to Pilarcitos Creek. Fine sediment destroyed habitat by covering riffles
and filling pools, and by creating a flat and shallow sandy substrate (Marston 1993).
Two land uses, roads and agriculture, are likely a large source of human-induced or anthropogenically-
generated sediment in the watershed. PWA (1996) noted the historic channel modifications to Pilarcitos
Creek in the Middle Pilarcitos region as a part of agricultural development. SFPUC provided a partial
map of roads for the entire Pilarcitos watershed (Figure 28). Based on quick review of aerial photographs,
it appears this road map is incomplete. This coverage is sufficient to identify unpaved roads along
Pilarcitos Creek above Highway 92 and along most of the tributaries (Nuff, Corinda Los Trancos,
Apanolio, Madonna, Mills, Upper Arroyo Leon). Balance Hydrologics (2003b) performed an inventory of
sediment sources in the Apanolio watershed and noted many locations where poorly-maintained or failing
roads are contributing to sedimentation in the Apanolio Creek channel. Balance (2003a) also noted that
the Highway 92 road crossing (see Section 2.3.4) with Pilarcitos Creek may have increased the sediment
discharge measured in water year 2000.

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The 1996 Restoration Plan stated that approximately 400 acres of floodplain and hillslope are cultivated
for agriculture within the Pilarcitos Creek watershed (PWA, 1996). Top soil eroded from the farmed area
by sheet erosion is carried toward creeks, and in areas with no riparian buffer, the sediment contribution
from agriculture may be high. Agricultural runoff contributes to sedimentation in Apanolio Creek
(Balance 2003b). Aerial photographs reveal that much of the floodplain in Middle Pilarcitos is used for
agricultural purposes.
Grazing, agriculture and, more recently, urbanization, have changed the relationship between rainfall and
the resulting runoff that enters streams and rivers. As a watershed area becomes more intensively
developed, a greater proportion of rainfall appears as runoff (as opposed to infiltrating into the soil or
being trapped by vegetation), resulting in more frequent runoff events with greater volume and higher
peak flows. These flow regime changes disturb the channel equilibrium and often cause erosion of the bed
and banks. This process generally is known as hydromodification.
Impacts from hydromodification likely are greatest in Lower Pilarcitos and Corinda Los Trancos.
Increasing residential development in Half Moon Bay increases the impervious surface in Lower
Pilarcitos increasing the amount of runoff. Lower Pilarcitos is particularly susceptible to impacts from
hydromodification because the channel substrate is predominantly sand. The BFI landfill covers a
majority of the Corinda Los Trancos watershed ultimately reducing infiltration and therefore summer
flows. However, as noted above, the reduction in sediment in Corinda Los Trancos is subject to retention
structures which can fail. The Pilarcitos Quarry also increases runoff in the Nuff Creek watershed.
Land-use factors have not been evaluated in any systematic manner to date. PWA contacted the
Association of Bay Area Governments (ABAG) for a GIS coverage of land use in the watershed to help
quantify the impacts from various land uses. Delivery of this coverage is currently pending further
communication from ABAG, and it is beyond the scope of the current phase of the IWMP to develop a
land use map from aerial photographs. A more accurate sediment budget incorporating a current land use
coverage can be developed for the watershed to estimate which land uses are most significantly affecting
sediment delivery to Pilarcitos Creek and its tributaries.

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Table 9. Land Use Change and Associated Hydrologic and Geomorphic Effects
Change in Land Outcomes of Possible Hydrologic Possible Geomorphic
or Water Use Change Effect Effect
Drainage Increase in peak discharge. Increase of erosive stresses in
reconfiguration Decrease in lag times of the channel resulting in
(e.g., reducing the floods. increases in bank failures.
number of small Undermining of banks.
ephemeral Increase in sediment yield.
channels)
Homogenization of Reduction in the amount of Increase in erosive stresses in
land surface depression storage. Decrease the channel resulting in
in infiltration rates. Increase increases in bank failures.
in peak discharge. Decrease Undermining of banks.
in lag times of floods. Increase in sediment yield.
Compaction of land Decrease in infiltration rates Increase in surface runoff and
coupled with increase in some increase in bank erosion.
overland flow Some increase in sediment
yield.
Vegetation removal Increase in sheetwash erosion.
on floodplain Rilling.
Removal of native Reduced evapotranspiration Riparian areas are eliminated or
STREAMSIDE stream-side and interception. degraded. Bank resistance
AGRICULTURAL vegetation decreases resulting in increased
ACTIVITIES number and extent of failures.
Increase in sediment yield.
Water diversions Decrease in flow between Riparian areas are eliminated or
for agricultural points of diversion and degraded. Bank resistance
purposes and disposal, lowering soil decreases resulting in increased
groundwater moisture in riparian zone. number and extent of failures.
pumping Concentrating of ground Increase in sediment yield.
water discharge to a point
source.
Stream channels Increased flood damage if Changes in channel geometry
put in artificial culverts are undersized. and sediment load. Increases in
channels or culverts Increased backup flows. stream channel stability
Increased downstream peak problems. Aggradation and
flood flows if channelized. flooding upstream of project
structure. Loss of floodplain
storage.
Removal of trees or Reduction in infiltration. Riparian areas are eliminated or
vegetation Reduction in degraded. Bank resistance
evapotranspiration and decreases resulting in increased
interception. Increase in number and extent of failures.
streamflows. Increase in sediment yield.

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Change in Land Outcomes of Possible Hydrologic Possible Geomorphic
or Water Use Change Effect Effect
Increase in Decrease in infiltration. Increase in erosive stresses in
impervious surfaces Increase in streamflows. the channel resulting in
(including roads) Increase in peak discharge. increases in bank failures.
Decrease in lag times of Undermining of banks. Gully
floods. Decrease in water formation. Increase in sediment
table levels. Flow yield.
concentration.
INCREASING
Stream channels Increased flood damage if Changes in channel geometry
LEVEL OF
put in artificial culverts are undersized. and sediment load. Increases in
URBANIZATION
channels or culverts Increased backup flows. stream channel stability
Increased downstream peak problems. Aggradation and
flood flows if channelized. flooding upstream of project
structure. Loss of floodplain
storage.
Removal of trees or Reduction in infiltration. Riparian areas are eliminated or
vegetation Reduction in degraded. Bank resistance
evapotranspiration and decreases resulting in increased
interception. Increase in number and extent of failures.
streamflows. Increase in sediment yield.
Roads have significant hydrologic and sedimentary influences on the channel network. Roadcuts intercept
slow natural runoff and routes water into ditch drainage systems that increase flood magnitude, decrease
baseflows, and typically transport large volumes of road and ditch sediment. Road drainage systems also
can increase the rate of erosion from hillslope swales that receive road drainage from cross-draining
culverts. Road systems can also route road sediment directly into tributary channels. Improperly designed
or maintained roads also present an increase risk of landslides in the form of hillslope failures. The most
damaging road systems tend to be stream-adjacent roads (which have very high rates of sediment
delivery), and mid-slope roads (which typically have large hydrologic impacts and sediment delivery
rates. Well-designed road systems that are properly maintained can significantly reduce these potential
impacts. At the present time, only limited information for existing road conditions is available, although
anecdotal evidence of poor road conditions is abundant within the watershed.
4.2.3 Channel Form and Erosion
A number of different factors influence channel morphology including channel bed and bank material,
cross-section geometry (width and depth), and channel slope. We used an easily attainable parameter,
channel slope, to qualify channel form in the Pilarcitos watershed based on the slope classifications by
Montgomery and Buffington (1997) (Figure 29). Channel gradient is a useful parameter in this case for

12/28/07 28
defining the transport potential of the various tributaries in the Pilarcitos watershed. This method
discounts local variations in slope and is intended solely for watershed-scale evaluation of channel slope.
A review of current and historic aerial photos suggests that few large-scale channel planform changes
have occurred over the last 6 decades. Planform changes typically occur in response to deposition of
coarse sediment or accumulations of large woody debris, both of which are limited in the watershed.
Coarse sediment and woody debris also provide important habitat structure, and the lack of structure may
also be a limiting factor in habitat creation within the watershed.
Smaller subwatersheds have steeper channels that are typically dominated by cascade, step-pool, and
plane-bed morphologies (Figure 29). For example, Corinda Los Trancos and Nuff Creek maintain at least
a 2.5% slope until the confluence with Pilarcitos Creek. A steeper gradient can contribute to higher
velocities and shear stresses in the stream channel, resulting in greater potential for sediment transport.
Larger subwatersheds and portions of Pilarcitos Creek have less steep channels more typically associated
with pool-riffle morphology (Figure 29). Pilarcitos Creek maintains a slope of less than 2.5% below the
confluence with Albert Canyon, and Lower Arroyo Leon maintains a similar slope below the confluence
with Mills Creek. Where channel slope decreases, the potential for sediment deposition and storage
increases. Sediment deposition in the form of channel bars can be beneficial for habitat, flow diversity,
and channel bed stabilization. However, it also can contribute to channel aggradation, which can cause
lateral migration and bank erosion.
Another factor that may contribute to sediment is the degree of channel bed instability throughout the
watershed. Channels throughout the watershed are incised, possibly due to long-term land-use impacts
that have altered flow patterns, contributing to higher peak flows. Streamside riparian management may
also play a role in reducing bed stability within the watershed.
4.2.4 Sediment Discharge Rates
In order to estimate the relative sediment contribution from select subwatersheds, we developed a rough
estimate of subwatershed peak flows by using data from preliminary estimates of total annual flow for
each subwatershed (Table 6) with peak runoff frequencies for the Pilarcitos Creek at Half Moon Bay
station (Figure 30). Peak runoff values were assigned to each subwatershed based on the relative
proportion of total annual runoff for that subwatershed. Flow values were then input into the sediment
rating curves identified by Balance (2003a) to provide preliminary estimates of sediment discharge for
various flow probabilities. Given the limits of the available data, we could only apply this approach to
peak flow return periods less than 5 years. This is not an ideal estimate, but is the best approach given the
available data.
Results from this estimate are provided in Tables 9 and 10, and indicate that the two primary sources of
sediment in the Pilarcitos Watershed are from Apanolio Creek and Upper Pilarcitos Creek below Stone

12/28/07 29
Dam. Balance (2003a) reported that measured rates of sediment discharge as a function of flow from the
Apanolio and Corinda Los Trancos subwatersheds were the highest for the watershed. However, Corinda
Los Trancos actually has among the lowest total sediment discharges when flow is considered. Corinda
Los Trancos, Upper Arroyo Leon, and Mills Creek each experience sediment bedloads that are roughly 3-
5% of the loads of Apanolio Creek when normalized by flow, based on our preliminary estimate.
The results from Apanolio and Upper Pilarcitos may be somewhat high relative to their actual
contribution, given the method for deriving our estimates. A more accurate estimate of sediment
discharge for each subwatershed may be possible through analysis of 15-minute flow data that will more
accurately capture peak flow magnitude and storm duration values. Such data may be available through
special request to the USGS and Balance Hydrologics (who report such data being available in their 2001
and 2003 reports). Such data was not available at the time of this writing.
Table 10. Preliminary Estimate of Normalized Bedload Production Rate

Normalized Bedload Production Rate (tons/day)
Mills Ck
Return at Upper Corinda
Period Exceedance Higgins Arroyo Pilarcitos Los
(yrs) Probability Road Leon at Sare Apanolio Tancos
1.5 0.67 59 93 1,800 2,000 85
2 0.5 68 107 2,000 2,300 95
2.5 0.4 118 186 3,400 3,900 148
5 0.2 381 602 374
Table 11. Preliminary Estimate of Normalized Suspended Load Production Rate

Normalized Suspended Load Production Rate (tons/day)
Mills Ck
Return at Upper Corinda
Period Exceedance Higgins Arroyo Pilarcitos Los
(yrs) Probability Road Leon at Sare Apanolio Tancos
1.5 0.67 460 370 1,000 3,000 240
2 0.5 530 430 1,100 3,500 270
2.5 0.4 920 740 1,800 6,000 410
5 0.2 3,000 2,400 1,000

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5. RIPARIAN ECOLOGY
The riparian plant community native to the Pilarcitos watershed includes of a wide diversity of native
plant species. Historically, the vegetation structure included a riparian tree over story, a shrub layer and a
dense herbaceous layer with no bare ground, supporting diverse and abundant wildlife. Riparian
vegetation also helps to stabilize stream banks and reduce inputs of sediment to the streams from bank
erosion or by acting as a filter for sediment from upslope or adjacent land. Reduced streamflow and lack
of summer baseflow can affect riparian stand recruitment and evolution. Beneficial riparian species like
willow, alder and maple require wetter riparian conditions. Dryer riparian soils promote non-native
species like Eucalyptus and various conifer species, which offer lower habitat value for instream fisheries.
Riparian vegetation provides shade that regulates thermal heating of the stream. However, shade also
reduces the light that allows algae and rooted aquatic plants to grow, and so may also reduce the
abundance of invertebrates that act as food for steelhead. Light also allows fish to more easily feed on
drifting insects, and increased water temperature increases fish digestive rates. Therefore, a cool,
unshaded stream actually provides the best fish growth, provided it is not too cold to significantly slow
food digestion. In cooler northern or higher elevation streams cool and unshaded habitats are common,
but along the Central Coast the proper balance between the food benefits of sun and the increased
metabolic cost for steelhead associated with stream heating are harder to achieve. The native streamside
trees are mostly deciduous (alders, willows, bigleaf maples). So, the dense riparian canopy may be open
in spring and late fall to allow algal growth and more efficient feeding. Evergreen forests (redwood,
tanoak, and Douglas fir) in upstream riparian corridors and invasive eucalyptus in downstream riparian
corridors provide perennial canopies that reduce stream productivity and may reduce fish growth.. The
deciduous trees also provide softer, nontoxic, more easily digestible leaves that support invertebrates
(shredders) that also serve as fish food. Although the riparian corridor along many of the Pilarcitos
watershed streams has been narrowed by urban and agricultural development, stream shading is generally
quite high because the channels are usually narrow and incised.
Riparian and upland trees (particularly large native evergreens) are also a source of large wood to the
stream, where logs, rootwads and branches provide valuable escape cover (especially for larger juvenile
steelhead), overwintering shelter from high stormflows and scour objects for deeper, more complex pools.
In many small stream channels of the watershed, even small logs (4” diameter or less) can provide
significant improvement of pool habitat in terms of increased escape cover. Logs also can produce
logjams, which can offer important structural habitat components.

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Assessment of riparian conditions is based on available information from previous watershed analyses,
various biological reports, and electronic databases. Following a thorough search, information about the
condition of vegetation communities has principally relied on existing literature such as the Restoration
Plan (PWA, 1996) and the SFPUC’s 2002 Peninsula Watershed Management Plan (EDAW 2002), as well
as database sources such as the California Wildlife Habitat Relationship System (CWHR) and the
California Natural Diversity Database (CNDDB) (CNDDB 2007). Information from the online version of
the California Native Plant Society’s Inventory of Rare and Endangered Plants of California was used in
conjunction with CNDDB to evaluate potential occurrences of special-status plant species within the
watershed. The minimum mapping unit of vegetation data in the SFPUC’s 2002 Peninsula Watershed
Management Plan was approximately 0.10 acre (EDAW 2002). Riparian habitat in the Restoration Plan
(PWA, 1996) was mapped using aerial orthophotos at 1:400 scale and three days of reconnaissance
between July and September 1995 on property where access was granted (PWA 1996). Vegetation data
from CWHR is derived from Landsat Thematic Mapper satellite imagery, high altitude color infrared
photography and ground surveys resulting in a minimum mapping unit of approximately 250 acres.
5.2 DISTRIBUTION AND COMPOSITION OF NATIVE PLANT ASSOCIATIONS
A wide range of vegetation types occur within the Pilarcitos Creek Watershed varying with elevation,
aspect, soil types, disturbance regimes, and previous land use (Figure 31). The predominant vegetation
community throughout the watershed is a mosaic of coastal scrub and annual grassland (CWHR 2005).
Agricultural cropland and urban areas dominate the lower elevations adjacent to Pilarcitos Creek, while in
the upper watershed patches of coniferous forest comprised of Douglas fir (Pseudotsuga menziesii) and
coast redwood (Sequoia sempervirens) as well as areas of mixed chaparral are present (CHWR 2005,
EDAW 2002). These upland plant communities provide important habitat components for special-status
wildlife in the watershed, and some include rare plant species and community types. However, in
accordance with the H. T. H.'s scope of work, this assessment is primarily focused on the vegetation
within the riparian corridors of the Pilarcitos Creek Watershed.
Riparian vegetation in the Pilarcitos varies between the upper and lower portions of the watershed.
Arroyo willow (Salix lasiolepis) and red alder (Alnus rubra) are the dominant trees in the riparian
corridors of the watershed. However, the upper watershed also includes a few additional closely
associated habitats along the riparian corridor; these include the coastal scrub, chaparral, and Douglas fir
forest. The riparian plant communities in the watershed have previously been classified by various
sources within different parts of the watershed (PWA 1996, EDAW 2002). Riparian areas in the lower
watershed have been classified into 5 categories according to the dominant tree species: Willow Riparian
Forest, Willow-Alder Riparian Forest, Willow-Mixed Riparian Forest, Eucalyptus-Alder Riparian Forest,
or Eucalyptus Grove (Figure 32 and Figure 33) (PWA 1996).

12/28/07 32
The tree canopy of Willow Riparian Forest areas consists of arroyo willow and yellow willow (Salix
lutea). This habitat is found along Pilarcitos Creek west of Highway 1 and along the lower reaches of
Corinda Los Trancos Creek. Scattered red alder, Monterey pine and blue gum eucalyptus trees also occur
within the lower reaches of Pilarcitos Creek. Dominant understory shrubs typically include California
blackberry (Rubus ursinus), poison oak (Toxicodendron diversilobum), and red elderberry (Sambucus
racemosa). The herbaceous understory in this riparian habitat is dominated by non-native invasive
species, particularly Cape ivy (Delairea odorata) and poison hemlock (Conium maculatum).
Red alder (Alnus rubra), arroyo willow (Salix lasiolepis), and yellow willow (Salix lutea) dominate the
upper canopy of Willow-Alder Riparian Forest. Examples of this type of riparian forest occur along the
lower reaches of Apanolio Creek, Madonna Creek, upper Arroyo Leon, and Mills Creek (Figure 32 and
Figure 33). In addition to the dominant tree species, California buckeye (Aesculus californicus), blue gum
eucalyptus (Eucalyptus globulus), Monterey cypress (Cupressus macrocarpa), and Douglas fir occur in
scattered locations. The shrub layer is dominated by California blackberry, poison oak, and coast
elderberry. Additional shrub species that are present include coffeeberry (Rhamnus californica),
snowberry (Symphoricarpos albus var. laevigatus), thimbleberry (Rubus parviflorus), and creek dogwood
(Cornus sericea). Dominant plant species in the herbaceous understory include stinging nettle (Urtica
dioica), sword fern (Polystichum munitum), and hedge nettle (Stachys bullata). Non-native invasive
species such as Cape ivy and poison hemlock are also prevalent in the herbaceous understory.
Where arroyo willow and yellow willow are equally dominant with a number of other species in the upper
canopy layer, the riparian habitat was classified as Willow-Mixed Riparian Forest. Examples of this
habitat occur along lower reaches of Arroyo Leon and Pilarcitos Creeks (Figure 32). Here, associated
dominant tree species include red alder, Monterey pine (Pinus radiata), and blue gum eucalyptus. The
shrub layer is dominated by California blackberry and poison oak with some red elderberry and coyote
bush (Baccharis pilularis) present. The herbaceous understory is primarily composed of non-native
invasive species (see below); however a few native understory species are present including, mugwort
(Artemisia douglasiana), bedstraw (Galium sp.), wild cucumber (Marah fabaceus), and hedge nettle
(Stachys palustris arenicola).
In riparian areas where eucalyptus has invaded and is out-competing native riparian tree species, the
corridor was previously classified as either Eucalyptus-Alder Riparian Forest, or simply as a Eucalyptus
grove (PWA 1996). Examples of this forest type occur along portions of the lower reaches of all 7 creeks
in the watershed (Figure 32 and Figure 33). Examples of extensively invaded corridors are evident at the
junction of Nuff Creek, Pilarcitos Creek, and along sections of Mills Creek. Although this riparian forest
type presently represents a unique forest composition and structure that provides certain wildlife habitat
functions, it may be better to consider it as an invaded type of the previous 3 historic riparian habitat types
(i.e. Willow Riparian, Willow-Alder Riparian, or Willow-Mixed Riparian Forest). According to this
approach, Eucalyptus-Alder Riparian Forest would represent an example along the continuum from
Willow Riparian Forest to pure Eucalyptus Grove. Considering the riparian habitat this way may be

12/28/07 33
helpful in assessing the restoration potential of a given patch of riparian forest, whereby the least invaded
areas may be the most cost-effective to restore to a willow or willow-alder type of riparian forest.
Sites along low gradient reaches of the tributaries of the Pilarcitos with access to shallow groundwater or
that experience frequent flooding represent good candidate sites to restore Willow or Willow-Alder
Riparian Forest. One example that could serve as a reference site for restoration planning purposes can be
found upstream of the ponds at Higgins Rd. on Arroyo Leon Creek (Go Native 2002). Tall red alder and
yellow willow dominate the tree canopy in this location. The tall shrubs in this area include arroyo
willow, creek dogwood, and red elderberry. Additional shrubs include thimbleberry and California
blackberry. The herbaceous understory includes western sword fern, California bee plant (Scrophularia
californica), hedge nettle, and stinging nettle. Above the riparian corridor begins the coastal scrub
community, which includes coyote bush, twinberry (Lonicera involucrata), coffee berry, sticky monkey
flower (Mimulus aurantiacus), lizard tail (Eriophyllum staechadifolium), yerba buena (Satureja
douglasii), coast madia (Madia sativa), mugwort (Artemisia vulgaris), and pink flowering current (Ribes
sanguineum).
Riparian forest in Upper Pilarcitos, above the junction with Nuff Creek and Pilarcitos Creek, has mostly
been classified according to 2 types of dominant species: arroyo willow or red alder (EDAW 2002). The
understory of the red alder dominated areas includes salmonberry (Rubus spectabilis) and red elderberry
in the shrub layer. Riparian areas with significant amounts of white alder (Alnus rhombifolia) also occur
between Stone Dam and Pilarcitos Reservoir. In addition, the main channel of Pilarcitos Creek is shown
bisecting a patch of old growth Douglas fir / redwood forest as well as running through coastal scrub and
chaparral near the headwaters. These upland plant communities within the upper watershed occur in close
proximity to the narrow riparian corridor and may be influenced by riparian conditions. Some riparian
reaches in the upper watershed include California bay (Umbellularia californica), big leaf maple (Acer
macrophyllum), and Douglas fir in the tree canopy with hazel (Corylus cornuta) in the understory shrub
layer. Similarly, coast live oak (Quercus agrifolia) woodlands grow close to the riparian community near
the headwaters of Pilarcitos Creek and side tributaries above Pilarcitos Reservoir. Where coastal scrub
grows close to the riparian corridor in Upper Pilarcitos, it can consist of coyote brush, coffeeberry, and
thimbleberry.
5.3 INVASIVE PLANT SPECIES
Invasive non-native species are present in all 7 tributaries of Lower Pilarcitos, frequently occurring with
high percent cover (PWA 1996). Blue gum eucalyptus and Cape ivy appear to be the most pervasive and
cover the greatest surface area (Figure 34 and Figure 35). Additional invasive species that occur in the
watershed include: poison hemlock, bristly ox-tongue (Picris echioides), black mustard (Hirschfeldia
incana), Italian thistle (Carduus pycnocephalus), milk thistle (Silybum marianum), periwinkle (Vinca
major), garden nasturtium (Tropaeolum majus), pampas grass (Cortaderia spp.), French broom (Genista
monspessulana), and small-leaf spiderwort (Tradescantia fluminensis) (Figure 34 and Figure 35). The
most highly invaded areas appear to be along lower Nuff Creek near the confluence with Pilarcitos Creek,

12/28/07 34
Mills Creek, and the lower reaches of Pilarcitos Creek. Detailed information about the amount and
location of invasive species are not available for the upper watershed.
5.4 SENSITIVE PLANT COMMUNITIES
Riparian corridors and wetland habitats are considered high priority habitats by the CDFG CNDDB and
are subject to federal, state, and county regulations. Freshwater wetland habitat does exist in the
watershed; however it has not been mapped in detail for the majority of the watershed. For example,
freshwater wetland habitat occurs at the upstream end of Pilarcitos Reservoir, behind Stone Dam, and in
numerous locations along riparian floodplains. Vegetation removal and stream alteration are subject to
permits according to Section 1600 of the California Fish and Game Code and Section 404 of the federal
Clean Water Act. In addition, these habitats are considered sensitive according to the San Mateo County
General Plan (DEP 1986) and Local Coastal Program (LCP) (ESASM 1998) and are accorded
consideration within the County grading ordinance. The LCP defines riparian corridors according to the
limit of riparian vegetation. According to this definition, riparian vegetation must include at least 50%
cover of any of the following plant species: red alder, jaumea (Jaumea carnosa), pickleweed (Salicornia
spp.), big-leaf maple, narrow-leaf cattail (Typha angustifolia), arroyo willow, broad-leaf cattail (Typha
latifolia), horsetail (Equisetum spp.), creek dogwood, black cottonwood (Populus balsamifera
trichocarpa), and box elder (Acer negundo) (Figure 36).
5.5 SPECIAL-STATUS PLANT SPECIES
A search was conducted to determine whether any special-status plant species might occur within riparian
habitats within the watershed. A query of CNDDB records for the 3 USGS quadrangles that cover the
watershed (Montara Mountain, Woodside, and Half Moon Bay) revealed a total of 36 plant species that
have historically occurred within these 3 quads. Many of these species occur outside of riparian habitats
in the serpentine grassland and maritime chaparral located in the upper watershed. A cross-reference
using the CNPS inventory showed that only 5 of these species occur within riparian habitats such as those
that occur within the Pilarcitos Watershed (CNPS 2007) (Table 12). All 5 species are included on List 1B
by CNPS indicating that they are rare and endangered in California and elsewhere. However, due to the
way that coastal scrub, chaparral and Douglas fir forest intergrade with the riparian corridor, especially in
the upper watershed, some additional species may occur in close proximity to the riparian corridor that
were not detected by this method. Many of the species known to occur in this vicinity are said to occur in
coastal prairie, coastal scrub, or Valley and foothill grasslands, habitats that occur closely adjacent to the
riparian corridor. For example, fragrant fritillary (Fritillaria liliacea) has been reported as occurring,
“near the headwaters of Pilarcitos Creek,” even though it is not listed as occurring in riparian habitats
according to the CNPS inventory (PWA 1996). One recorded occurrence for western leatherwood (Dirca
occidentalis) lists associated species as coyote bush, poison oak, hollyleaf cherry (Prunus ilicifolia),
Pacific black snakeroot (Sanicula crassicaulis), and wild cucumber, and a second record lists the
associated species as Douglas fir, coffeeberry, and mountain mahogany (Cercocarpus betuloides)
(CNDDB 2007). These lists of associated species are not comprised of typical obligate riparian species.

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This suggests caution when considering riparian habitat requirements too narrowly for special-species
plant species within the watershed since many are known to occur within both riparian and adjacent
habitats, such as coastal scrub. Table 12 shows each species’ rarity status and their associated habitats.
Among the 5 special-status plant species known to occur in riparian habitats within the vicinity of the
watershed, only Hickman's cinquefoil (Potentilla hickmanii), western leatherwood, and fragrant fritillary
have been reconfirmed in recent years (Table 12). Hickman’s cinquefoil is known to occur just outside
the watershed near the town of Montara (Figure 37). A population of Hickman’s cinquefoil was found at
this location as recently as 2002. Western leatherwood is known to occur within the watershed and has
been reconfirmed in 2001 (Table 12 and Figure 37). Davidson's bush mallow (Malacothamnus
davidsonii), Parry’s tarplant (Centromadia parryi ssp. Parryi), and coastal marsh milk-vetch (Astragalus
pycnostachyus var. pycnostachyus) have not been reconfirmed since prior to the early 1920s, though
CNDDB records still consider them to be extant. Among these three species only Davidson’s bush
mallow has been recorded as ever occurring within the Pilarcitos Watershed, while the other 2 species
were recorded outside the watershed, along the coast, northwest of the watershed boundary. Field notes in
the CNDDB record state that recent surveys for coastal marsh milk vetch were limited and that the
species needs further study to confirm its presence and extent in the vicinity (CNDDB 2007).

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Table 12. Conservation Status, Habitat Information, and Occurrence Records of Special-Status Plant Species Reported from the Vicinity
of the Pilarcitos Creek Watershed within Riparian Habitats
Rarity Confirmed Bloom

Common Scientific Family Life Form Status Habitat Elevation Status Period Quad
coastal marsh Astragalus Fabaceae perennial List 1B.2 Coastal dunes, 0 - 30 m 1902 outside Apr-Oct Half Moon
milk-vetch pycnostachyus var. herb S2.2 G2T2 Coastal scrub, watershed, Bay
pycnostachyus Marshes and Pillar Point
swamps (coastal vicinity
salt, streamsides)
Parry’s tarplant Centromadia Asteraceae annual herb List 1B.2 Chaparral, Coastal 2 - 420 m 1921, exact May- Montara
parryi ssp. parryi S2.2 G4T2 prairie, Meadows location Nov Mountain
and seeps, Marshes uncertain,
and swamps northwest of
(coastal salt), watershed
Valley and foothill near Pacifica
grassland, Vernally
mesic, often
alkaline sites

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western Dirca occidentalis Thymelaeaceae deciduous List 1B.2 Broadleaved upland 50 - 395 m 1954 & 1975 Jan-Mar Montara
leatherwood shrub S2S3 G2G3 forest, closed-cone in upper Mountain
coniferous forest, watershed
Chaparral, 2001 in upper
Cismontane watershed
woodland, North
Coast coniferous
forest, Riparian
forest in mesic
brushy slopes,
mesic sites, mostly
mixed evergreen &
foothill woodland
communities
Davidson's Malacothamnus Malvaceae deciduous List 1B.2 Chaparral, 15-355 m 1901 in upper Apr- Woodside
bush mallow davidsonii shrub S2.2 G2 Cismontane watershed Sept
woodland, Coastal
scrub, Riparian
woodland in sandy
washes

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Hickman's Potentilla Rosaceae perennial List 1B.1 Coastal bluff scrub, 10-135 m 1933 near Apr-Aug Montara
cinquefoil hickmanii herb S1.1 G1 SE Closed-cone Half Moon Mountain
& FE coniferous forest, Bay 1996-
Meadows and seeps 2002 outside
(vernally mesic), of watershed,
Marshes and north of
swamps Montara
(freshwater)
freshwater marshes
seeps, small streams
in open or forested
areas along coast
fragrant Fritillaria liliacea Liliaceae bulbiferous List 1B.2 Cismontane 3-410 m 2003 in upper Feb-Apr Woodside
fritillary herb S2.2 G2 woodland, Coastal watershed
prairie, Coastal
scrub, Valley and
foothill
grassland/often
serpentinite

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Key to Table
CNPS List Definitions

List 1A=Plants presumed to be extinct in California
List 1B= Plants rare and endangered in California and elsewhere
List 2= Plants rare and endangered in California, more common elsewhere
List 3= Plants about which more information is needed, review list
List 4= Plants of limited distribution, watch list
0.1-Seriously threatened in California (high degree/immediacy of threat)

0.2-Fairly threatened in California (moderate degree/immediacy of threat)
0.3- Not very threatened in California (low degree/immediacy of threats or no current threats known)
State and Federal Listing

FE=Federally Endangered
SE=State Endangered
Global Ranking The global rank (G-rank) is a reflection of the overall condition of an element
throughout its global range.
G1 =Less than 6 viable element occurrences (EOs) OR less than 1,000 individuals OR less than 2,000
acres.
G2 = 6-20 EOs OR 1,000-3,000 individuals OR 2,000-10,000 acres.
G3 = 21-80 EOs OR 3,000-10,000 individuals OR 10,000-50,000 acres.
G4 =Apparently secure; but factors exist to cause some concern; i.e., there is some threat, or somewhat
narrow habitat.
G5 =Population or stand demonstrably secure to ineradicable due to being commonly found in the world.
State Ranking The state rank (S-rank) is assigned much the same way as the global rank, except state
ranks in California often also contain a threat designation attached to the S-rank.
S1 = Less than 6 EOs OR less than 1,000 individuals OR less than 2,000 acres
S2 = 6-20 EOs OR 1,000-3,000 individuals OR 2,000-10,000 acres
S3 = 21-80 EOs or 3,000-10,000 individuals OR 10,000-50,000 acres
S4 = Apparently secure within California; this rank is clearly lower than S3 but factors exist to cause
some concern; i.e. there is some threat, or somewhat narrow habitat.
S5 = Demonstrably secure to ineradicable in California.

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6. WILDLIFE HABITAT
This section describes habitat conditions for special-status wildlife species within the Pilarcitos
watershed. Species of interest include steelhead (Oncorhynchus mykiss), San Francisco garter snake,
California red-legged frog, western pond turtle, riparian-associated bird species, and marbled murrelet.

In order to determine the existing conditions of special-status wildlife species within the watershed, we
conducted literature and database searches to identify known locations of species occurrences and
reviewed aerial photographs to map potential aquatic habitat for special-status reptiles and amphibians.
Habitat assessments and electrofisher sampling of juvenile steelhead were performed in a portion of the
watershed in 1995 to rate habitat conditions for steelhead and suggest restoration actions for the
Restoration Plan. Since then, additional fisheries studies have been conducted that improve our
understanding of previously sampled reaches and/or provide information on areas not previously
investigated. In addition, barrier modification and other actions have been taken that modified conditions
compared to 1996; details of these actions are provided in a subsequent section.
Because San Francisco garter snake, California red-legged frog, and western pond turtle rely upon aquatic
and wetland habitats, we quantified the distribution of ponded environments within the watershed. USDA
National Agricultural Imagery Program Aerial photographs taken in the spring of 2005 were used to
assess potential aquatic breeding sites (e.g., areas that pond water); ponds were digitized using ArcGIS
9.1. Aerial photographs taken in 2005 were chosen because ponding of water at potential aquatic habitat
for these species is more evident in the spring or early summer during a year of at least average rainfall;
rainfall was above average in 2005. We felt it necessary to identify pond habitats throughout the
watershed, as this habitat type was not explicitly quantified, or discussed, in the Restoration Plan (PWA,
1996) and represents important breeding and/or foraging habitat for California red-legged frogs, San
Francisco garter snakes, and western pond turtles.
Information on special-status riparian-associated birds was derived from previous reports, the CNDDB,
and the San Mateo County Breeding Bird Atlas (Sequoia Audubon Society 2001). Marbled Murrelet
occurrences in the Pilarcitos Watershed were obtained from previous reports on murrelet surveys on
SFPUC lands (Albion Environmental 1998, CDM and Merritt Environmental Consulting 2003, URS
Corporation 2004, Avocet Research Associates 2005, 2006).
6.2 STEELHEAD
Steelhead habitat requirements change as they go through different life phases. Adult steelhead need to
have access to their natal streams. This means that streams must be free of barriers to migration, as the
majority of spawning occurs in the upper reaches of tributaries. Adults also need access to spawning
gravel in areas free of heavy sedimentation with adequate flow and cool, clear water. For spawning,

12/28/07 41
steelhead utilize gravel that is between 0.5 to 6 inches in diameter, dominated by 2 to 3 inch gravel.
Escape cover such as logs, undercut banks, and deep pools for spawning adults is also important.
For steelhead eggs and pre-emergent fry, the most important consideration in terms of habitat is cool
water with adequate dissolved oxygen. Fine sediment will smother developing eggs, so the area must not
have excessive fine silt or sand. During their first summer, juvenile steelhead are typically found in
relatively shallow areas with cobble and boulder bottoms. Juvenile steelhead prefer areas including
woody debris accumulation such as logs or tree roots. Cover structures such as boulder clusters and root
wads provide both summer and winter rearing habit. As juvenile steelhead grow, pools become an
important habitat component. The best pools for habitat are those with abundant escape cover in the form
of large woody debris, undercut banks, root masses, and large boulders.
Cool, clean water is essential for the survival of steelhead during all portions of their life cycle. Elevated
water temperatures (>70° F) can greatly impair growth rates of juvenile steelhead if adequate food is not
available. Warmer water also holds less dissolved oxygen and increases a fish´s susceptibility to disease
(Flosi 1998).
This section summarizes available steelhead abundance and habitat information for the Pilarcitos
watershed. The first three sub-sections describe significant factors limiting steelhead habitat, and the final
sub-section summarizes habitat conditions in the Pilarcitos stream system by reach.
6.2.1 Flow Diversions
As described above, the Pilarcitos Reservoir and Stone Dam complex divert substantial amounts of winter
and spring flow to San Andreas Reservoir and Upper Crystal Springs Reservoir (SFPUC) and through a
pipeline to CCWD. The winter diversions probably reduce passage conditions for adult steelhead
migrating in Pilarcitos Creek, especially upstream of tributaries closest to Stone Dam (ENTRIX 2006b).
The CCWD wells may also reduce winter and spring flows in Upper Pilarcitos (Kennedy/Jenks 2006).
Reduced spring flows and lack of early summer bypass flows at Stone Dam hinder smolt out-migration in
spring and the growth of juvenile steelhead in spring and early summer.
The effects from Pilarcitos Reservoir and Stone Dam could be mitigated with improvements to the
diversion and with a change in how the diversions are managed. The City and County of San Francisco
and the SFPUC are reviewing the operations of Pilarcitos Reservoir and Stone Dam as part of their
Program Environmental Impact Report for Water Systems Improvements.
Numerous smaller diversions on Apanolio and Pilarcitos Creeks and on Arroyo Leon also affect spring
and summer stream flows and smolt out-migration and juvenile rearing growth and density. Lower
Pilarcitos Creek and Arroyo Leon are normally dry by September in average to dry years due to several
appropriative and numerous riparian water diversions. Diversion dams are also potential impediments to
adult steelhead spawning access and may also affect smolt out-migration. The diversion on Apanolio

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Creek (barrier 1) normally blocks adult access to all potential spawning and the best rearing habitat on
that stream. The timing of closure of the dam/pond on Apanolio Creek (barrier 2) is a potential smolt and
adult passage issue. The timing of closure at the two ponds (the Johnson Ranch or Guisti Ponds) on
Arroyo Leon was a smolt passage issue and a major factor in eliminating their operation.
6.2.2 Culverts and Fish Passage
Culverts are potentially important barriers to adult steelhead migrating upstream. Even when originally
constructed at channel grade level, down cutting frequently occurs at the downstream ends of culverts,
especially in sandy bedded streams like those within the Pilarcitos Creek watershed. This produces
“perched” culverts. A private culvert on Arroyo Leon and an historical bridge on Mills Creek were
modified in 1997-1998 for adult passage following recommendations in PWA (1996). However, the
(vortex) boulder weirs used to remediate the culverts were also subject to channel down-cutting and still
posed difficulties to steelhead passage in 2007 (Alley 2007bc). A private culvert (barrier 3) on Apanolio
Creek was modified in 2007 for fish passage with boulder weirs that will be subject to down-cutting in
the future. Modest partial barriers to adult steelhead movement exist at Highway 92 on Pilarcitos Creek
(planned for modification by CalTrans) and at Higgins-Purissima Road on Arroyo Leon.
Most importantly, stream culverts can block or impede upstream access for adult steelhead, preventing
seeding of upstream habitats. In response to density induced competition, juvenile steelhead generally
disperse downstream in late spring and summer and saturate downstream habitats, including reaches
where spawning conditions are poor. However, in some cases, barriers can also have effects by blocking
juvenile fish from upstream movements. These movements are probably only ecologically significant
(limiting to steelhead smolt production) where lower reaches become too warm for rearing or where fish
move upstream to or from winter high flow refuges. Even when lower reaches dry up, it appears that fish
generally concentrate in deep pools (which also later dry up), rather than move upstream. The apparently
low relative significance of juvenile movement in many cases is an important issue, since providing
passage for large, high-jumping adults can often be accomplished relatively easily and cheaply compared
to providing passage for juvenile fish.
6.2.3 Rearing Habitat
Production of young-of-year (YOY) steelhead in the watershed is probably most affected by the lack of
adult spawning access to habitats by made-made barriers and by the quality of spawning habitat, with the
best habitat concentrated in upstream reaches. However, steelhead must grow to at least 5-6 inches in
length before smolting and entering the ocean to grow and mature to adulthood, and smaller smolts have
much lower marine survival than larger smolts (Bond, 2006). Production of these larger juveniles is more
important than production of smaller YOY fish in terms of producing returning adults.
For most habitats within the Pilarcitos Creek watershed (and most other central coast streams (Smith
2006) juvenile steelhead must spend 2 years rearing in stream habitat to reach smolt size. That also means

12/28/07 43
that they must survive 2 winters, and overwintering habitat, in the form of large, complex pools with large
instream wood, backwaters and cobble and boulder substrate, is scarce. Yearling and older steelhead are
scarce compared to YOY steelhead throughout stream habitat in the Pilarcitos watershed (and many other
central coast watersheds), and the shortage of high quality habitat for them limits smolt and adult
abundance (Smith 2006).
Where stream habitat is more productive for aquatic invertebrates and summer stream flows are higher (to
allow feeding on drifting insects), YOY steelhead can reach smolt size in a single summer. This occurs in
high summer stream flow sections of the lower San Lorenzo River and Soquel Creek watersheds (Alley
2007b) and where summer stream flows are augmented downstream of reservoirs, like in Uvas Creek in
Santa Clara County (Smith and Li 1983). Lagoons can also provide for fast steelhead growth by providing
relatively warm, but extremely productive rearing habitat with abundant food sources (Smith 1990, Bond
2006). Nearly all YOY steelhead rearing in Central Coast lagoons reach smolt size in one summer.
Lagoons/estuaries provide important spring and summer rearing habitat and saltwater transition habitat
for smolting steelhead in many coastal watersheds (Smith 1990; Bond 2006). For Pilarcitos Creek, the
lack of summer stream flow to the mouth prevents the development of a lagoon in all but the wettest
years. Even in systems where summer water is available, the beach configuration and sandbar dynamics
are major factors in the quality of a lagoon for steelhead rearing in spring and summer. Where scour
objects (cliffs, meanders, bridge abutments) are present, the stream tends to scour deep pools that provide
residual habitat when the sandbar is open in late winter and spring. These pools provide habitat for
feeding by smolts migrating to the ocean and may provide a substantial spring growth increment to
improve ocean survival. In addition, the deep pockets, or ponding behind early partial sandbars, trap
heavier salt water on the bottom during high tides and provide habitat where smolts (especially smaller
ones) can gradually adjust to salt water (by going up and down in the water column). This salt water
acclamation improves their survival upon ocean entry (Smith 1990). Sandbar dynamics are also a factor in
lagoon ecology, with early summer sandbar formation damming up inflow and producing productive,
mixed, (but often relatively warm) freshwater lagoons (Smith 1990, Bond 2006). Not only does Pilarcitos
Creek normally lack a summer lagoon, due to lack of inflows, it does not provide a spring feeding or salt
water transition habitat for smolts because of a lack of residual depth when the sandbar is not in place;
small smolts produced in upstream portions of the watershed probably have minimal transition habitat
and low ocean survival (Bond 2006).
In some systems, early sandbar closure in spring can block smolt out-migration, and delayed opening in
the winter of drought years can delay adult upstream access. In addition, a broad, shallow open lagoon
mouth may restrict successful fish passage to extreme high tide periods. At Pilarcitos Creek the lagoon is
small and relatively small stream flows from Pilarcitos Creek (and Frenchmen’s Creek) help to keep the
sandbar opened . However, passage through the shallow open lagoon and across the broad lagoon mouth
may often be a problem for migrating fish; predation in such a shallow system is an additional threat.

12/28/07 44
In the Pilarcitos Creek watershed, stream flows are low, fine sediment is abundant and insect production
is generally low. No lagoon is usually present. The only habitat that provided for abundant fast-growing
steelhead was the two on-channel ponds on Arroyo Leon (the Johnson Ranch or Guisiti Ponds), which
acted like productive “upstream lagoons.” Sunlight penetrating these ponds produced algae and an
abundance of invertebrate food that allowed YOY and yearling steelhead to grow to large size, despite the
higher metabolic cost of living in warmer water (Smith 2001 and 2002). The unusually large size of the
fish produced in these ponds means that they would have a high probability of returning as adults (Bond
2006). Large size is also especially important in order to survive the transition to salt water in a system
like Pilarcitos Creek, where no brackish estuary exists in spring to aid the transition to salt water. If the
regulatory issues surrounding operation of these ponds could be resolved, these important habitats might
again contribute substantially to steelhead production in the watershed. Depending upon how it is
operated, the on-channel pond on Apanolio Creek also has the potential to produce numerous large
juvenile steelhead.

12/28/07 45
6.2.4 Stream Habitat Summary
The Restoration Plan concluded that the most limiting factor to steelhead population was low streamflow
resulting from water diversion, which hinders adult spawning migration, smolt out-migration, and
juvenile rearing conditions. Although the fishery assessments reported in the Restoration Plan were
performed in a wet year (1995), summer stream flows were still low enough to limit steelhead abundance
throughout the watershed. Fine sediment throughout the watershed also limited spawning and rearing
habitat quality.
Water quality is normally not a major issue for fisheries for most of the watershed. In the running streams,
water temperatures are relatively cool, dissolved oxygen is rarely a problem due to mixing in riffles, algae
is controlled by shading and limited availability of hard substrates (rather than nutrient levels), and
rooted aquatic plants such as watercress provide important habitat for fish and aquatic invertebrates as
long as open water exists. Turbidity from road runoff during winter and spring storms is a problem for
Albert Canyon and Pilarcitos Creek downstream of the Highway 92 crossing (Smith 1998 and 1999).
Water quality is a potential problem in ponded systems such as the ponds on the Arroyo Leon (Smith
2001 and 2002), the pond on Apanolio Creek, and when a lagoon is present at the mouth. In those habitats
growth of algae can produce dissolved oxygen depression during extended periods of fog due to algal
respiration and a lack of photosynthesis (Smith 2001 and 2002). However, the abundance of algae in
those habitats is major reason for their abundance of invertebrates and the rapid growth of steelhead.
“First flush” and other runoff from the town of Half Moon Bay would affect only the lowermost reaches
of Arroyo Leon and Pilarcitos Creek; these reaches are often dry in summer and rear few or no steelhead
in most years. However, the issue could be much more important if streamflows in lower Pilarcitos Creek,
including to the lagoon, are increased in the future.
Table 13 summarizes the habitat ratings from the 1996 Restoration Plan and subsequent studies. On the
Pilarcitos mainstem, stream habitat quality and fish abundance generally increased upstream. Twelve of
17 spawning habitat reach ratings within the watershed were poor, and only 3 were rated as fair.
However, with additional investigations of four upstream reaches since, spawning on upper Pilarcitos
Creek, upper Arroyo Leon and Albert Canyon are rated as fair or better (Table 13). In 1996 rearing
habitat was rated fair-good in only 3 reaches out of 17, but 3 additional reaches investigated since are
rated as fair-good or better (Table 13). The Bongard pond above the second barrier in Apanolio Creek and
the 2 ponds on Arroyo Leon provided, and still potentially could provide, the only “good” or better
rearing habitat for juvenile steelhead.

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Table 13. Existing Steelhead Rearing, Spawning and Migration Conditions for Stream Reaches in Pilarcitos Creek Watershed.
New information since PWA 1996 shown in bold. Includes source of new information and primary limiting factors (in approximate order of
importance). Ratings are “on a curve,” as conditions within the watershed are relatively poor (low stream flow, high sediment levels) compared to
most other central coast watersheds.
Stream Up Spawning Rearing Down New Info Sources Limiting Factors

Reach Migration Migration
Pilarcitos Creek
Reach 1 fair-good none poor fair flow, fine sediment,

(upstream of Half spawning, pool dev.
Moon Bay)
Reach 2 Good poor-fair poor-fair fair-good flow, fine sediment,

upstream to Corinda spawning, pool dev.
Los Trancos Creek
Reach 3 Good fair fair fair-good Smith 1998, 1999 flow, fine sediment pool
upstream to Hwy 92 development
Reach 4 fair-good fair-good fair-good fair-good Smith 1996, 1998, 1999 flow, fine sediment,
upstream to Stone Dam Trihey 1995, 1996 passage?
ENTRIX 2006a,b
Reach 5 None fair fair N/A ENTRIX 2006a,b access, fine sediment, flow
upstream to Pilarcitos
Lake

12/28/07 47
Arroyo Leon Creek
Reach 1 good poor poor fair-good flow, fine sediment

Below dams
Reach 2 good poor-fair Ponds: fair-good Smith 2001, 2002 reservoir open/close
Ponds very good- (delayed operations and
excellent+ closure) infrastructure, water
quality
stream: poor flow, fine sediment
Reach 3 good fair poor-fair fair-good Smith 2001-2002 flow, fine sediment
upstream to drop
structure
Reach 4 fair— poor-fair fair? fair-good Alley 2007bA flow, fine sediment
upstream to Higgins barrier
Rd. modified but
partially
failed
Reach 5 fair-good? fair? fair? fair-good Smith 2006 (limited) fine sediment?, flow?
upstream of Higgins
Rd.

12/28/07 48
Mills Creek
Reach 1 good poor-fair fair-good fair-good fine sediment, flow

upstream to historic
bridge
Reach 2 poor- fair fair-good fair-good Alley 2007bA flow, sediment

Bridge upstream to bridge
gradient increase & barrier
small dam modified, but
failing
Reach 3 good- fair-poor poor-fair fair-good Alley 2007bA flow, sediment

upstream barriers
modified
Madonna Creek
Reach 1 fair poor poor fair-good sediment, flow

upstream to barrier
Reach 2 none poor poor-good? fair sediment, flow

12/28/07 49
Apanolio Creek
Reach 1 good poor? fair? fair-good sediment, flow

upstream to diversion
dam
Reach 2 none-poor poor? fair? fair-good access, sediment, flow

upstream to pond
Reach 3 good at poor-fair stream: fair poor-good Alley 2007ba access, sediment flow
Pond to flashboard present
dam apron below
BFI boundary
pond: very pond open/close

good? operations
Reach 4 none-poor fair poor poor-good Alley 2007ba access, sediment pool
flashboard dam development flow
apron upstream 1.1
miles

12/28/07 50
Nuff Creek
Reach 1 ? poor poor fair sediment, pool

upstream to quarry development
barrier
Reach 2 none poor poor fair access, sediment pool

development
Albert Canyon
Reach 1 fair-good good poor-fair good Smith 1998, 1999 flow, fine sediment from
½ mile to falls Hwy 92, turbidity
Reach 2 none fair poor-fair N/A access, flow

(no fish
present)
Note: Revision of Table 10 from PWA 1996

12/28/07 51
The following sub-sections summarize steelhead habitat conditions for each stream reach in the Pilarcitos
watershed.
6.2.4.1 Lower & Middle Pilarcitos Creek

CDFG conducted a survey of Pilarcitos Creek from Stone Dam to the ocean in 1977 during a severe
drought. Continuous surface flow existed only in approximately the ½ mile downstream of Stone Dam.
The mainstem was intermittent to channel mile 4 and was completely dry downstream (Zatkin 2002).
Even in recent average years, the creek is normally dry near Highway 1 by late summer. A CDFG survey
by seasonal aide Judi Ford upstream to above the Sare property in 1985 found the channel dominated by
sand, dewatering by diversions at temporary dams common, and riparian vegetation removal occurring
(Zatkin 2002). Conditions were similar in 1995 (PWA 1996) and at the present time. Streamflows are
generally highest upstream, and immediately below the Apanolio Creek confluence. Substrate conditions
are best immediately downstream of Albert Canyon, but even there habitat conditions are not good. Most
of the steelhead habitat downstream of Albert Canyon on Pilarcitos is dominated by shallow glides or
runs (Smith 1999). Pools are scarce. During even small storms, this reach received turbid runoff from
Albert Canyon. Substrate is predominantly sand with the addition of larger gravels and cobbles from
Albert Canyon.
6.2.4.2 Lower Arroyo Leon

Steelhead were common during a CDFG survey of Arroyo Leon in the fall of 1958. On-channel reservoirs
(Johnson Ranch or Guisti Ponds) were in place, and angling use was assumed to be heavy in lower
reaches and assumed to be planted with hatchery fish (Zatkin 2002). A CDFG Survey of Arroyo Leon in
1992 (Jennifer Nelson) found rainbow trout, steelhead, and frogs (Rana sp.) above the impoundments
(Zatkin 2002). A large Eucalyptus log-jam 100 ft long was observed above the impoundments, and lower
reaches were used as an urban dumpsite. In 2000 and 2001 a partial log jam was present at the upper end
of the upper pond, at an abandoned flashboard dam.
The two on-channel impoundments provided the best habitat conditions for steelhead in the Pilarcitos
watershed in 2000 and 2001 (Smith 2002). Fish reared in the impoundments were large (145-244 mm
Standard Length). Almost all captured fish had silvery coloration, lacked parr marks, and had deciduous
scales and black edges to their caudal fins. These strong smolt characteristics probably indicated that fast
growth in the reservoirs, and cooling conditions in November triggered early preparation for
smoltification. Smith (2002) noted early smoltification in fast-growing lagoon fish in previous lagoon
studies, allowing them to emigrate to the ocean within a month of sandbar breaching. Reservoir densities
were much higher than in stream habitat immediately upstream of them, producing 10 times the number
of smolts (and much bigger fish) as an equivalent length of stream habitat in 2001. Relatively few 2-year
old smolts were trapped in the reservoirs. About 2,000 steelhead of smolt size were estimated from 0.3
miles of reservoir in the year 2000 compared to 35 smolt-sized fish captured in 0.1 miles of nearby
stream. Fishermen were commonly seen at the upper reservoir during water quality sampling. These
reservoirs could account for the majority of smolt production in Arroyo Leon subwatershed in years like
2000.

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These ponds have not been operated since 2001, due to regulatory restrictions (see section 4).
6.2.4.3 Mills Creek

A CDFG Survey of Mills Creek in the Fall of 1958 indicated excellent spawning gravel without
confirming data (Zatkin 2002). Steelhead/rainbow trout were also observed. Streambed conditions in
1995 (PWA 1996) and 2007 (Alley 2007bA) were dominated by sand. Spawning habitat was judged to be
at best fair, but improved somewhat upstream. A severe barrier at the historical bridge was modified in
1997 and 1998 (see section 4); modification partially failed by 2007 (Alley 2007bA), and the site remains
a significant impediment to adult steelhead movement.
6.2.4.4 Upper Arroyo Leon

A severe culvert barrier to fish passage existed in Arroyo Leon above the mouth of Mills Creek. It was
modified in 1998 for passage and was assessed in 2007 (see section 4). Despite partial failure of the
modifications (see section 4), passage is now suitable for adult steelhead during high winter storms. The
culvert at Purissima-Higgins Road required a jump to enter in 1995, but was at grade in 2006, and easily
passable in winter. With both barriers passable, adult steelhead can access habitat in Upper Arroyo Leon.
Rearing and spawning were rated as “fair” in the Restoration Plan (PWA 1996), based only upon
conditions observed immediately up and downstream of the two barriers.
6.2.4.5 Apanolio Creek

Apanolio Creek has higher summer streamflow than other portions of the watershed, because of the sandy
granite geology of the upper watershed. However, the stream channel is dominated by sand and the
channel is relatively small. The first recent survey of the upper portion of the stream on BFI property was
conducted in November and December 2007 (Alley 2007ba). Alley found the channel to be sandy, narrow
(mostly 3-5 feet wide in fall) and incised, with poor pool development (average depths of 0.6 feet and
maximum depths averaging only 0.9 feet). Densities of resident rainbow trout were low, with fish
inhabiting mostly small pools that constituted only about 30% of the habitat in one sampled segment and
10% in another. An impassable bedrock falls would block fish migration about 1 mile upstream on the
BFI property, but 2 man-made drop structures that were judged potentially significant steelhead passage
impediments are also present in the reach. Three fish passage barriers were identified in this subwatershed
downstream of the BFI property in 1995 (PWA 1996) and are described below in Section 4. The upper
barrier was modified for fish passage in 2007, but will not be reachable by migrating steelhead until the
lowermost barrier is modified. An additional barrier, a perched apron for a flashboard dam, was
discovered by Alley (2007B). The barrier, immediately downstream of the BFI property, was at grade in
1995, but the channel has since downcut about 5 feet on the downstream side. It would now probably be
impassable to migrating steelhead except during extreme floods.
Based upon the high densities of juvenile steelhead and rapid growth rates in the Arroyo Leon ponds
(Smith 2002), the best potential steelhead rearing habitat in the Apanolio Creek watershed would be in the
Bongard on-channel pond, if it were operated in a “fish-friendly” manner (regulated timing of opening

12/28/07 53
and closure, to insure adult and smolt passage) and if the downstream barrier 1 were modified to allow
steelhead passage to the pond.
6.2.4.6 Corinda Los Trancos, Nuff & Madonna Creeks

In the PWA (1996) report, Madonna, Corinda Los Trancos, and Nuff creeks were discounted as steelhead
resources but contributed summer streamflow and were significant sediment sources. Corinda Los
Trancos had very poor habitat conditions. Nuff Creek is relatively small and ditch-like. The small size of
the channel is apparently due to attenuated winter storm flows, due to the quarry upstream. There was a
concrete/wood dam 0.3 miles up Madonna Creek. It had very limited steelhead habitat because of its very
low streamflow. It was intermittent even in the wet year of 1995.
6.2.4.7 Albert Canyon

Albert Canyon contains a small tributary along the uphill portion of Highway 92. Sites immediately up-
and downstream from Albert Canyon, were sampled for CalTrans in November 1998 and 1999 (Smith
1998 and 1999). Steelhead may access only about ½ mile of Albert Canyon Creek, downstream of a
boulder falls. However, because of the shale and sandstone geology of the watershed, this tributary has
abundant gravels and cobbles and relatively good spawning habitat. Fine sediment in runoff from
Highway 92 is a problem for winter turbidity levels and for fine sediment within spawning gravels. The
tributary is probably a very important spawning site that seeds much of the rearing habitat downstream in
Pilarcitos Creek. Gravels, cobbles and suitable spawning gravels were common, unlike in most of
Pilarcitos Creek. In the very wet first sampling year (1998) juvenile steelhead densities were relatively
high in this small stream due to relatively good pool and escape cover development. In 1999 (an average
rainfall year), fish density was about two-thirds less, reflecting the effect of low summer stream flows that
are typical of the creek.
6.2.4.8 Pilarcitos Creek Between Highway 92 and Stone Dam

An apron and drop structure under Highway 92 are a significant partial barrier to adult fish passage. They
will apparently be modified by CalTrans to improve fish passage (see section 4).
In November 1992 CDFG biologist Jennifer Nelson surveyed the reach between Stone Dam and
Pilarcitos Reservoir. Pools were very shallow; the deepest being 1.5 feet deep and most averaging about 9
inches. The streambed consisted of sand and was not conducive to spawning or food production. Only 4
rainbow trout were observed.
Access to CCWD property was not available to the PWA team in 1995, but 3 sites were sampled by
electrofisher by Smith (1996) and reported as Appendix C to the Restoration Plan. The CCWD property
on Pilarcitos Creek provided some of the best steelhead spawning and rearing habitat in the watershed
(Smith 1996). There was relatively good substrate that would produce good insect abundance if flows
were increased. There was good pool development and the streambanks and channel were stable, unlike
most other incised reaches in the watershed. Rearing conditions were fair-togood. Spawning was fair-to-

12/28/07 54
good. Migration was good for adults and fair-to-good for smolts. Juvenile steelhead densities were
between 12 and 23 smolt-sized juveniles/ 100 ft.
Balance Hydrologics (1997) summarized results from PWA (1996) and Smith (1996) in their report, but
did no additional fish sampling. Trihey and Associates, under contract with the SFPUC, conducted habitat
and electrofishing sampling on CCWD and SFPUC properties, downstream of Stone Dam in 1995 and
1996 (Trihey 1995 and 1996). A qualitative habitat assessment conducted Aug 4, 1995 by Trihey &
Associates (1995), identified habitat conditions consisting of mostly shallow run with probably less than
20% pool habitat in a well-developed riparian corridor. They surveyed 1.5 miles of habitat including three
x 100 ft segments that were electro-fished. Most fish captured were YOY’s, 37-97 mm fork length. Older
fish were 114-179 mm fork length. They estimated that approximately 2,500 fish/mile inhabited the
property with 3,700 juvenile trout estimated. Riffles contained gravels and some cobbles. Fine textured
streambed probably made aquatic insect production low. Several small pools were observed at 1 to 1.5
feet in depth (did not specify maximum depth or average depth). Trihey & Associates (1995) concluded
that other than fine sediment, there was good to very good habitat for juvenile trout, although their
observations do not seem to support this conclusion.
Trihey & Associates (1995) recommended several habitat improvements, including:

periodic channel maintenance/flushing flows.
flow augmentation in dry years
better roadway drainage and road maintenance with graveling
placement of Douglas fir logs across the stream to cause scour pools
gravel augmentation (addition of imported, rounded river gravels) to increase spawning gravel
acquisition of a stream conservation easement downstream of the CCWD property in order to
restore the riparian corridor.
These studies were in general agreement between years and with Smith (1996) that spawning and rearing
conditions in the reach were somewhat better than further downstream on Pilarcitos Creek. However, low
summer stream flows and abundant fine sediment (granitic sand) limited rearing habitat. Substrate
conditions were best (more gravels, cobble and boulders) in the first mile downstream of Stone Dam,
where gradient was higher and sediment input was reduced by sediment retention at Stone Dam.
However, this portion of the reach had the lowest summer stream flows because seepage flow past the
dam was minimal and west bank tributary inputs were further downstream. Smith (1998 and 1999)
sampled a site at the bottom of the reach (immediately upstream of Albert Canyon Creek on the Sare
property) in 1998 and 1999, finding habitat sandier and fish scarcer than further upstream during previous
sampling in the 1995 and 1996.
Habitat conditions were investigated and an evaluation of the relationship of flow to rearing habitat,
spawning habitat and passage downstream of Stone Dam was conducted in 2004 by ENTRIX (2006a,
2006b), as Appendices A and B in the 2006 Kennedy/Jenks report. These studies indicated that an

12/28/07 55
increase in summer stream flow would substantially improve rearing habitat conditions for steelhead.
However, the quantitative results of the flow study should be considered preliminary because of
questionable methods associated with: choosing cross-section locations to model, the low number of
cross-sections modeled, selection of the reference grade conditions, assumptions made for habitat
suitability and passage criteria, and the exclusion of escape cover as factor to be modeled for rearing
habitat as a function of streamflow.
6.2.4.9 Pilarcitos Creek Upstream of Stone Dam

ENTRIX (2006a) evaluated habitat conditions and sampled fish (resident rainbow trout) in 2004 in the
reach between Stone Dam and Pilarcitos Reservoir. They concluded that spawning and rearing habitat and
existing fish populations were generally similar to those downstream of Stone Dam. Low stream flows
and fine sediment limited rearing habitat quality. Pools were relatively scarce and shallow, but escape
cover (in the form of overhanging riparian vegetation) was common. The report concluded that an
additional 2.3 miles of stream could be provided for steelhead above Stone Dam, which would add 27%
to the total length of Pilarcitos Creek mainstem accessible to steelhead. No upstream passage at Stone
Dam presently exists, but options for providing passage were evaluated in Kennedy/Jenks (2006). An
environmental constraint in laddering Stone Dam is that if too much bypass flow is required to provide
up- and downstream steelhead passage over the dam in winter and spring, there will be insufficient bypass
flows available for rearing habitat below the dam in summer and fall. Without these bypass flows,
Pilarcitos Creek may become intermittent between the dam and the CCWD well field during the dry
season.
6.3 HERPETOFAUNA
Riparian habitat supports a diverse assemblage of flora and fauna and is considered one of the most
important wildlife habitats in North America. Riparian corridors are used by a wide variety of wildlife for
breeding, foraging, and dispersal. The Restoration Plan (PWA, 1996) focused on riparian conditions and
highlighted potential restoration and management strategies for the tributaries and associated vegetation
communities throughout the watershed. Non-fish, special-status wildlife species that were identified in the
plan as known to occur within, or in close proximity to, the watershed included San Francisco garter
snakes, California red-legged frogs, and western pond turtles; however, the plan included relatively little
information on these species. Furthermore, although the riparian corridor represents important habitat for
all of the aforementioned species (especially for foraging and dispersal), ponded and slow moving
backwater pools are considered the primary habitats for these species. Incised channels, dense forest
cover, and/or high winter and spring flows that are common along creeks within the watershed provide
marginal to poor habitat for this group of herpetofauna. Rather, ponded environments, deep slow moving
waterways, and off-channel pools represent very important habitat for these species. In addition to
suitable aquatic habitat, appropriate upland habitat is also an important component of maintaining viable
populations of these species.

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6.3.1 California Red-legged Frog
(Rana aurora draytonii). Federal Status: Threatened; State Status: Species of Special Concern
The California red-legged frog is a member of the family Ranidae within the order Anura, and is one of
two subspecies of the red-legged frog (Rana aurora). The draytonii subspecies was included as a
Category 1 candidate species in the U.S. Fish and Wildlife Service’s Annual Notice of Review in
November 21, 1991. On June 24, 1996, the California red-legged frog was officially listed as a
Threatened species under the auspices of the Federal Endangered Species Act (FESA) (USFWS 1996)
based largely on a significant range reduction and continued threats to surviving populations. Factors
related to declines in populations of red-legged frogs include the degradation or loss of habitat attributed
to agricultural practices, introduced plants and animals, livestock grazing, mining, water diversions and
impoundments, water quality, recreation activities, timber harvesting, and urbanization.
California red-legged frogs utilize a wide variety of aquatic and terrestrial habitats throughout their
historic range. Larvae, juveniles, and adult frogs occur in natural lagoons, dune ponds, pools in or next to
streams, streams, marshlands, sag ponds, and springs, as well as human-created stock ponds, secondary
and tertiary sewage treatment ponds, wells, canals, golf course ponds, irrigation ponds, sand and gravel
pits containing water, and large reservoirs.
California red-legged frogs are typically associated with perennial, or near perennial, water and the
general lack of introduced aquatic predators such as crayfish (Pacifastacus leniusculus and Procambarus
clarkii), bullfrogs (Rana catesbeiana), and centrarchid fishes such as green sunfish (Lepomis cyanellus),
bluegill (Lepomis macrochirus), and largemouth bass (Micropterus salmoides). The stream habitats
observed to contain the largest densities of red-legged frogs are associated with pools at least 27 inches
deep with overhanging willows and an intermixed fringe of cattails (Typha spp.), tules or sedges, though
adults are commonly found in shallower pools with vegetative cover, and young-of-the-year metamorphs
are commonly found in shallow runs and riffles. In addition, red-legged frogs are sometimes found in
high densities in stock ponds lacking in vegetation around their margins. The continued persistence of
red-legged frog populations may depend largely on the existence of ponds, springs or pools that are apart
from perennial streams. Such habitats provide the continued basis for successful reproduction and
recruitment into nearby drainages that may lose frog populations due to stochastic events such as extreme
flooding or droughts. During wet periods, especially in the winter and early spring, red-legged frogs can
move a mile or more between aquatic habitats. This movement often occurs across seemingly
inhospitable frog habitat like roads, open fields, and croplands. This type of movement, which is best
documented in mesic coastal areas, may result in frogs occupying aquatic habitats isolated from known
frog populations.

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Locations of Known Occurrence of California Red-legged Frog in the Watershed
There were 5 CNDDB records and 5 anecdotal accounts (Swaim Biological 2006; PWA 1996) of
California red-legged frogs occurring within the Pilarcitos Creek Watershed at specific locations (Figure
38). Field notes from CDFG surveys conducted over the last 70 years included several accounts as well;
however, specific locality data was not included and several of the accounts simply listed “frogs” (Zatkin
2002). Therefore, these accounts were not included in the species maps. Adult and recently
metamorphosed California red-legged frogs were observed in artificial, in-stream ponds on Arroyo Leon
at Johnson Ranch (Smith 2002) as well as ponded water above Stone Dam (Swaim Biological 2006)
indicating these sites are likely being used for breeding. Both of these sites are artificial impoundments
and their hydrology can be changed by different management strategies. The Arroyo Leon ponds have
historically been open for the majority of the year and were closed during the late spring in order to pond
water during the summer months (Jerry Smith, pers. comm.). The fact that water was not ponded prior to
late spring in these ponds suggests that California red-legged frogs may have been breeding later than
normal (California red-legged frogs typically breed in the late winter and spring). These ponds also
supported a large number of steelhead smolt (Smith 2002). If California red-legged frogs are indeed
breeding in these ponds, continued closure of the dams will enhance breeding and foraging habitat for this
species.
We reviewed the Seymour and Westphal 2000 study on amphibians in the Midpeninsula Regional Open
Space District Preserves in the Santa Cruz Mountains for the presence of California red-legged frog
occurrences in the Pilarcitos watershed (Seymour and Westphal 2000). Their study area just barely
extended into the focal area for the Pilarcitos Watershed Assessment (where the extreme edge of Purisima
Creek Redwoods OSP extends into the Arroyo Leon watershed), and they reported no California red-
legged frogs in this area.
6.3.2 San Francisco Garter Snake
(Thamnophis sirtalis tetrataenia). Federal Status: Endangered; State Status: Endangered The San
Francisco garter snake was one of the first reptiles to be listed under the FESA by the USFWS in 1967.
The San Francisco garter snake was also listed under the state Endangered Species Act in 1971 and is
fully protected species under the state Fish and Game Code. San Francisco garter snakes remain
threatened by continued habitat loss and degradation, as well as illegal collecting by reptile fanciers. San
Francisco garter snakes have been observed in a number of aquatic and terrestrial habitats throughout
their historic range, such as ponds, pools in or next to streams, streams, lakes and reservoirs. The presence
of adjacent upland areas with abundant small mammal burrows is also important as hibernation sites for
snakes during the winter. They prefer a dense cover of vegetation such as willows, bulrushes, cattails, and
tules. Adults mate during the spring and fall and young are usually born alive during late July to early
August. San Francisco garter snakes depend on frogs, particularly the threatened California red-legged
frog, for food. The San Francisco garter snake is restricted to San Mateo County and northern Santa Cruz
County, and has been found in creeks in Half Moon Bay.

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Locations of Known Occurrence of San Francisco Garter Snake in the Pilarcitos Creek Watershed
There were two CNDDB records and one anecdotal account (Swaim Biological 2006) of San Francisco
garter snakes occurring within the Pilarcitos Watershed (Figure 38). CNDDB records were along lower
Pilarcitos Creek, one near the mouth (recorded in 1988) and another in a weedy field between the creek
and Highway 92 approximately 0.15 miles east of Highway 1 (recorded in 2004). The only account higher
in the watershed is at the northeastern boundary of the eastern finger of Pilarcitos Reservoir (Swaim
Biological 2006). This area contains a relatively large area of freshwater marsh habitat that may be
suitable to support populations of San Francisco garter snake (Swaim Biological 2006).
6.3.3 Western Pond Turtle
(Emys marmorata). Federal Status: None; State Status: Species of Special Concern.
The western pond turtle is a medium-sized brown or olive-colored aquatic turtle, and is found west of the
Sierra Nevada crest and deserts and south to northern Baja California. Western pond turtles have
disappeared from a significant portion of their range due to habitat loss from agriculture, urbanization,
water development projects, and the introduction of non-native aquatic predators (i.e. fishes and
bullfrogs).
Pond turtles are normally found in and along riparian areas, although gravid females have been reported
up to a mile away from water in search of appropriate nest sites. The preferred habitat for these turtles
includes ponds or slow-moving water with numerous basking sites (logs, rocks, etc.), food sources
(plants, aquatic invertebrates, and carrion), and few predators (raccoons [Procyon lotor], introduced
fishes, and bullfrogs). Juvenile and adult turtles are commonly seen basking in the sun at appropriate
sites, although they are extremely wary animals and often dive into the water at any perception of danger.
Pond turtles have been known to colonize isolated stock ponds, and thus some long-distance overland
dispersal occurs. During the summer, they may aestivate in leaf duff, well away from riparian areas.
Adults breed in the spring and early summer (March - July). Typically, the female excavates a nest in
hard-packed clay soil in open habitats (usually on south-facing slopes) within a few hundred yards of a
watercourse; however, nests have been located up to 0.4 miles from water. The female then lays 1-15
eggs, which are left to incubate for three to four months.
Locations of Known Occurrence of Western Pond Turtle in the Watershed
There are no CNDDB records of western pond turtles within the Pilarcitos Watershed and only one
anecdotal account. The anecdotal account was from Jerry Smith who reported seeing several turtles at the
reservoirs in Arroyo Leon Creek (pers. comm., 2007). There are CNDDB records of western pond turtles
to the south and immediately east of the watershed.

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6.3.4 Discussion of Herpetofauna
Review of 2005 aerial imagery resulted in a detection of 41 off-channel ponds within the Pilarcitos
Watershed (Figure 38). These ponds represent potential breeding and aquatic foraging habitat for
California red-legged frogs, and aquatic/wetland foraging habitat for San Francisco garter snakes and
western pond turtles. The majority of ponds occurred in the floodplain along lower Pilarcitos Creek and in
the foothills throughout the southwestern region of the watershed. Nearly all of the ponded areas appear
to have been created as a result of anthropogenic activities (e.g., having earthen and concrete dams). It is
important to note that while this method (i.e., review of aerial photos) does allow for detection of ponds
over a broad spatial scale, other ponds distributed throughout the watershed (especially in heavily forested
regions) could be missed. The suitability of these off-channel ponds as habitat for these three special-
status species has not been assessed in detail, and site-specific conditions (e.g., predator abundance) likely
influence suitability. Nevertheless, many or most of these ponds should be considered potential habitat for
one or more of these species.
California red-legged frogs, San Francisco garter snakes, and western pond turtles are known to occur
within the Pilarcitos Watershed. With the exception of the pond behind Stone Dam and fringe wetland
habitat flanking the northeastern edges of Pilarcitos Reservoir, there is very little suitable breeding habitat
for California red-legged frogs in the northern watershed (region north of Pilarcitos Creek). This area
consists of incised creeks with dense riparian canopies and steep terrain. California red-legged frogs
require ponded or slow moving water devoid of predators, habitat that is uncommon in the northern
Pilarcitos Watershed. San Francisco garter snakes also require ponded, or slow moving water and rely
heavily upon California red-legged frogs as their prey base. Thus, while there is suitable dispersal habitat
(e.g., riparian corridors) for California red-legged frogs and San Francisco garter snakes, there are very
few high quality breeding areas in this part of the watershed. However, the lowland areas in the lower
watershed, and throughout the southwestern portion of the watershed from Pilarcitos Creek to Arroyo
Leon Creek, contain numerous ponds and low-gradient creeks (Figure 38). These areas likely provide
higher-quality habitat for California red-legged frogs and San Francisco garter snakes, and, in the ponded
areas, western pond turtles.
6.4 BIRD SPECIES
Two special-status, riparian/wetland-associated birds are known to breed within the riparian corridors of
the San Mateo Coast: the Saltmarsh Common Yellowthroat (Geothlypis trichas sinuosa) and Yellow
Warbler (Dendroica petechia brewsteri). Despite its common name, the Saltmarsh Common Yellowthroat
(a state species of special concern) actually breeds primarily in freshwater and brackish marshes, using
salt marsh habitats more during winter. This species has been confirmed breeding in a number of areas in
coastal San Mateo County (Sequoia Audubon Society 2001). It is expected to nest in weedy riparian
habitats and emergent vegetation along the lower portion of Pilarcitos Creek, and more sparingly in such
habitats (e.g., around ponds and in other areas providing emergent vegetation) farther upstream. It is
absent from the majority of the upper portion of the watershed due to the paucity of such habitats; for

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example, it was not recorded during bird surveys at Stone Dam Reservoir, 2004-2006, despite the
presence of some emergent vegetation there (URS Corporation 2004, Avocet Research Associates 2005,
2006).
The Yellow Warbler, a state species of special concern, is a riparian-associated bird species throughout
much of its California range. This species often breeds in riparian habitats dominated by cottonwoods
(Populus spp.) and willows (Salix spp.), but also uses riparian habitats dominated by alders (Alnus spp.),
western sycamores (Platanus racemosa), and other species. Although it is one of the most abundant
migrant warblers through the study area, it is much more scarce as a breeder, and it was not confirmed
breeding along Pilarcitos Creek during the San Mateo County Breeding Bird Atlas Project (Sequoia
Audubon Society 2001). Nevertheless, this species was recorded as a “probable” breeder in the atlas
blocks that included lower Pilarcitos Creek, and there is some potential for Yellow Warblers to nest in the
willow-dominated habitats in the lower portions of the watershed.
In addition, two raptors that are designated state species of special concern, the Cooper’s Hawk (Accipiter
cooperii) and Sharp-shinned Hawk (Accipiter striatus), could potentially breed in riparian habitat along
Pilarcitos Creek. Sharp-shinned Hawks were recorded in the Pilarcitos Creek area during the San Mateo
County Breeding Bird Atlas Project (Sequoia Audubon Society 2001), though breeding was not
confirmed in the watershed. A Sharp-shinned Hawk was recorded near Stone Dam Reservoir during a
breeding-season bird survey in 2005 (Avocet Research Associates 2005), and this species likely nests at
low densities in the watershed. San Mateo County Breeding Bird Atlas results suggest that Cooper’s
Hawks were unrecorded at least in the lower portion of the watershed during the Atlas Project (Sequoia
Audubon Society 2001). However, this species’ Bay-area populations have continued to increased in
recent years, and it is possible that this species nests in the study area at low densities, particularly in the
lower portion of the watershed.
The riparian habitats within the Pilarcitos Watershed support very high densities of breeding, wintering,
and migrant songbirds. Breeding species for which riparian habitats are particularly important include
Neotropical migrants such as the Warbling Vireo (Vireo gilvus), Black-headed Grosbeak (Pheucticus
melanocephalus), Swainson’s Thrush (Catharus ustulatus), Pacific-slope Flycatcher (Empidonax
difficilis), Wilson’s Warbler (Wilsonia pusilla), and Orange-crowned Warbler (Vermivora celata), as well
as permanent resident species such as the Winter Wren (Troglodytes troglodytes), American Dipper
(Cinclus mexicanus), Song Sparrow (Melospiza melodia), American Robin (Turdus migratorius), and
American Goldfinch (Carduelis tristis). During migration, large flocks of migrants occur in the riparian
habitats along Pilarcitos Creek.
6.4.1 Marbled Murrelet
(Brachyramphus marmoratus). Federal Status: Threatened; State Status: Endangered
The Marbled Murrelet is a small seabird that feeds in coastal oceanic waters and nests inland in mature
(often old-growth) forests dominated by conifers such as coast redwood and Douglas fir. This species

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nests from the Aleutian Islands in Alaska south along the Pacific Coast to Santa Cruz County, California.
Marbled Murrelets spend most of their time foraging in coastal waters, usually within 1 mile of shore.
However, when nesting (and occasionally during other times of the year), this species will fly inland to
suitable mature coniferous forest stands. Most nesting areas are fairly close to the sea, though the species
has been recorded in appropriate nesting habitat as far inland as 50 mi in Washington, 23 mi in northern
California, and 11 mi in central California (USFWS 1992).
Marbled Murrelets are semi-colonial, and multiple pairs may nest in a single stand of mature conifers.
Potential nesting habitat for Marbled Murrelets consist primarily of mature coniferous forests, or
occasionally younger coniferous forests with trees that provide relatively flat “platforms” on limbs high in
the crown. Such platforms consist of wide branches, mosses or lichens, mistletoe, or other structures
(Avocet Research Associates 2005). A single egg is laid on the platform. The loss of old-growth forests to
logging has been the primary cause of this species’ population declines.
The Pilarcitos Watershed occurs near (approximately 31 mi north of) the southern terminus of the
species’ range. The center of this species’ distribution at the southern end of its range has historically
been the Big Basin State Park area in Santa Cruz County, although numbers at this location have declined
precipitously in recent years (D. Suddjian, pers. comm.).
Designated Critical Habitat for the Marbled Murrelet includes an approximately 947-acre tract of land
owned by the City of San Francisco in Upper Pilarcitos (USFWS 1996). This area is located on the
southwest side of the creek between Pilarcitos Reservoir and Stone Dam Reservoir (Figure 39). Critical
Habitat for this species has been re-proposed, but the proposed Critical Habitat unit within the Pilarcitos
Creek Watershed would remain unchanged (USFWS 2006).
Locations of Known Occurrence of Marbled Murrelet in the Watershed
Although the Marbled Murrelet is regularly seen along the coast in the vicinity of Pilarcitos Creek, it was
not recorded inland within the watershed until 1998. In that year, a survey for this species along Cahill
Ridge, which forms the northeastern boundary of the watershed in the area downstream from Pilarcitos
Reservoir, recorded a single detection (Albion Environmental 1998). A follow-up survey in 2003
recorded 2 detections within the Pilarcitos Creek Canyon in the general vicinity of Stone Dam Reservoir
(CDM and Merritt Smith Consulting 2003a). A Marbled Murrelet monitoring plan for the Pilarcitos Creek
watershed between Pilarcitos Reservoir and Stone Dam Reservoir was developed by CDM and Merritt
Smith Consulting (2003b), and more intensive surveys were then conducted according to this plan, and
USFWS protocols, in 2004, 2005, and 2006.
No murrelets were recorded during the 2004 surveys (URS Corporation 2004). However, surveys in 2005
recorded a number of Marbled Murrelet detections (Avocet Research Associates 2005). Based on a
maximum count of 4-8 individuals, Avocet Research Associates (2005) estimated that 2 to 4 pairs of
Marbled Murrelets were nesting in a pure stand of mature Douglas fir west of Stone Dam Reservoir in

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2005. Flight behavior of these birds, which included birds flying within the crown of the trees in this
stand, was consistent with locally nesting birds. Although approximately 30% of known nests of this
species in North America have been from Douglas fir trees, most such nests are in association with coast
redwoods (Ralph et al. 1995). Avocet Research Associates (2005) noted that the forest stand with which
the Pilarcitos Creek birds were associated was thus possibly unique, at least in California, for consisting
purely of Douglas fir.
Surveys in 2006 again detected murrelets in Upper Pilarcitos Watershed, with a minimum estimate of 3
pairs (Avocet Research Associates 2006). Flight behaviors suggested that murrelets were nesting in the
same general portion of the watershed (i.e., the area southwest of the creek between Pilarcitos Reservoir
and Stone Dam Reservoir), but not in the same Douglas fir stand that was used in 2005. A reconnaissance
of the east-facing slope along the southwest side of the creek, and a review of aerial photographs, by
Avocet Research Associates (2006) indicated that potential nesting habitat was fairly extensive. The
approximate area mapped by Avocet Research Associates (2006) as providing potential nesting habitat
for Marbled Murrelets is shown on Figure 39.
Based on the locations and flight directions of murrelets detected in 2006, Avocet Research Associates
(2006) concluded that murrelets commuting between the upper Pilarcitos Creek watershed and the ocean
likely followed the creek during their commute flights.

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7. IMPLEMENTATION STATUS AND PROGRESS SUMMARY: 1996 RESTORATION PLAN
Opportunities and constraints were identified in the 1996 Restoration Plan. Constraints included low
streamflows resulting from surface diversions, near-channel wells and agricultural ponds. Other
constraints were sandy substrate that limited spawning and rearing habitat and fish barriers that restricted
or prevented steelhead migration to upper stream sections. Opportunities included increase streamflow
through voluntary agreements, modification of fish barriers, stabilizing streambanks and hillslopes,
removing exotic vegetation and replanting with natives, promoting setback and riparian buffers by
purchasing land or obtaining conservation easements.
PWA (1996) recommended alternatives for each sub-watershed. To summarize the implementation status
of these alternatives, we identified certain recommendations as common to all subwatersheds, specifically
removal and replacement of exotic plant species with native plant species, bank stabilization, and
maintenance of unpaved roads. Alternative recommendations targeted for specific locations within a
particular sub-watershed were kept separate. A summary of the current status of the alternative
recommendations can be found in Table 14 followed by a brief description of each of the ongoing and
completed alternatives.

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Table 14. Status Summary of Recommended Alternatives from 1996 Restoration Plan
Tributary Alternative Status Summary
All Provide resources for workshops Ongoing PCAC Forum on Restoration Projects in Watershed
(2/26/06)
Maintain unpaved roads Ongoing California State Parks - San Mateo State Parks Road-
Related Erosion Prevention Planning Project
Remove exotic plants and replace with native Ongoing Half Moon Bay Riparian Restoration Project - San Mateo
species County Natural History Association
Stabilize failing banks Unknown
Mills Creek and Modify Irrigation Ponds Ongoing Preliminary plans developed for modification of dams.
Arroyo Leon Ponds presently not in operation due to regulatory
restrictions. Alternative plans developed for off channel
ponds with diversion from the stream.
Modify barrier and stabilize banks at Historic Completed, but requires remedial Fish Passage Design by Clearwater Hydrology and
Bridge on Mills Creek work to function properly Watershed Science. Vortex weirs installed in 1997, but
failed in winter 1997-8. Reinstalled in 1998. Based upon
November 2007 assessment, most weirs have failed from
dislodged boulders, and fish passage is severely
restricted.
Modify Barrier 2 miles upstream on Mills Completed. Modified in 1998. Based upon November 2007
Creek assessment, still functioning properly
Modify barrier at Arroyo Leon culvert Completed, but requires remedial Fish Passage Design and Riparian Restoration by Fall
work to function properly Creek Engineering (FCE) with Swanson Hydrology and
Geomorphology, JGA and HES. Based upon November
2007 assessment, lower weir under driveway bridge
requires remedial work due to dislodged boulders, and
channel down-cutting below it requires action to provide
easy fish passage. Substantial hillslope erosion and
landsliding upstream of driveway bridge.
Stabilize gullies Unknown

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Tributary Alternative Status Summary
Apanolio Creek Modify lower fish passage barrier and Ongoing Fish Passage Design by Fall Creek Engineering. Future
stabilize banks funding and permits for implementation required.
Modify middle fish passage barrier and Ongoing Plans developed, but future funding and permits required.
stabilize banks
Modify upper fish passage barrier and Completed. May require future Modified with ungrouted boulder weirs and bridge in
stabilize banks remedial action. 2007. Based upon November 2007 observations of
similar structures on Arroyo Leon and Mills Creek, will
likely fail in first wet year (boulder movement likely,
channel down-cutting likely below downstream weir).
Pilarcitos Creek Increase instream flow below Stone Dam to Ongoing - Pilarcitos IWMP Kennedy/Jenks Final Operations Report - Feasbility
CCWD Wells Study
Increase instream flow from CCWD Wells to Ongoing - Pilarcitos IWMP Kennedy/Jenks Final Operations Report - Feasbility
Half Moon Bay Study
Install Vortex Weirs as a test of potential for Indirectly tested by fish passage Ungrouted Vortex Weirs appear to have limited potential
pool improvement. projects for pool development in the watershed.
Install Vortex weirs to replace drop structure Partially Complete Fish Passage and Culvert Design by WRECO
at Highway 92
Modify Fish Barrier at Stone Dam Ongoing - Pilarcitos IWMP Kennedy/Jenks Final Operations Report - Feasbility
Study
Estuary Reduce disturbance by constructing new Unknown
horse bridge
Increase instream flow to estuary Ongoing Would require study of possible use of reclaimed
wastewater.

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7.1 MAINTAIN UNPAVED ROADS
State Parks - Bay Area District was awarded approximately $70,780 for the San Mateo State Parks Road-
Related Erosion Prevention Planning Project in 2003. The goal of the project was to produce an erosion-
prevention plan for a 66 mile network of active surfaced and un-surfaced roads and legacy roads. This
project is an ongoing effort, and we were unable to find any reports on the progress.
7.2 REMOVE EXOTIC PLANTS AND REPLACE WITH NATIVE SPECIES
Half Moon Bay State Beach, part of State Parks, receives grant funding from the San Mateo County
Natural History Association, the San Mateo Countywide Stormwater Pollution Prevention Program
(STOPP), the California State Park Foundation, and the California Coastal Conservancy (CCC) to restore
riparian areas of lower Pilarcitos Creek, lower Frenchman's Creek, and the ponds of Venice Beach by
removing non-native vegetation, planting willows and other riparian plants along with native coastal
scrub, and removing trash. Members of the public can volunteer on a weekly basis to plant Beach Burr,
Beach Sagewort, Beach Primrose, Coast Buckwheat, Yarrow, Coyote Bush, Lizard Tail, Yellow Bush
Lupine, Evening Primrose, Figwort, Gum Plant, and Seaside Daisy. Education occurs through volunteer
recruitment publicity and training, interpretation display at the Half Moon Bay State Beach Visitor
Center, and post-project publicity and maintenance.
The major concern about exotic plants was with the extensive, expanding groves of Eucalyptus, which
reduce stream flow and suppress riparian native species more likely to control stream-bank erosion,
provide wildlife and fish habitat and provide edible leaves to support aquatic invertebrates. Discussions
did take place with companies that harvest trees for firewood. The hope was that removal could be done
for free as part of fire wood harvest. However, stump treatment to kill cut trees and revegetation efforts
would still result in substantial cost of Eucalyptus removal.
7.3 MODIFY BARRIER AND STABILIZE BANKS AT HISTORIC BRIDGE ON MILLS CREEK
AND AT DIVERSION DAM
A drop structure at a perched historic bridge on Mills Creek and a small flashboard dam/domestic
diversion structure further upstream were identified as barriers in the Restoration Plan (PWA, 1996). The
SWRCB and CDFG contracted Clearwater Hydrology and Watershed Science to conduct geomorphic
assessment and hydrologic and hydraulic analyses to document existing channel conditions and to assess
stable channel design characteristics at the 2 Mills Creek sites. The stable channel design included
removal of the instream concrete diversion dam and also correct a severe grade drop (9 ft.) produced by
scour below the historical bridge. Stable gradient and cross section geometry was constructed in the form
of a cascade channel through more than 1,000 ft. upstream and downstream of the historical bridge
barrier. The drop at the historical bridge was modified in 1997 with ungrouted boulder weirs that formed
a series of step pools up to the apron of the bridge. Storms in winter 1997-1998 damaged most of the
weirs in the sandy (bank and bed) channel, and the ungrouted boulder weirs were rebuilt in 1998. As of

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2007, the cascade reach remained stable, and riparian and wetland vegetation had established, including a
nearly closed overhead canopy. However, an assessment in November 2007 (Alley 2007bA) found
extensive damage to the weirs, with boulders dislodged, creating gaps in the weirs, and in one case a
tunnel between boulders where a weir was undermined. The jump to the failing lip of the bridge floor
would probably be passable to adult steelhead only at high (100 cfs) storm flows, when velocity over the
failing lip would be a problem. Remedial action would require moving boulders back into place and
grouting them together or using some other method to maintain their stability. The inclined floor of the
bridge culvert also poses a significant passage impediment that needs to be backwatered and/or modified
to improve steelhead passage.
The flashboard dam further upstream was removed in 1998, an infiltration gallery was built to provide
domestic water, and boulder weirs were installed to stabilize the channel. An assessment in November
2007 (Alley 2007bA) found the weirs to still be functioning properly.
7.4 MODIFY FISH PASSAGE BARRIERS AND STABILIZE BANKS ON APANOLIO CREEK
Final design plans have been completed for 2 barriers identified in the Restoration Plan (PWA, 1996) on
Apanolio Creek, and one barrier was modified in 2007. The lowermost (barrier 1, the Bongard diversion
dam) and uppermost (barrier 3, a perched culvert) were probably impassable under most conditions. The
middle barrier, an on-channel pond, is a partial barrier (apron and inclined culvert) when the dam is open.
The RCD was awarded a grant from the SWRCB to remove the uppermost barrier and improve riparian
habitat on Apanolio Creek (RCD 2007a), and this project was completed in September 2007. The goal of
this project was to restore steelhead trout passage in Apanolio Creek by removing an existing migration
barrier protecting existing species and habitat, and improving in-stream and riparian habitat in reaches
directly affected by the project while maintaining access to private property. However, steelhead are very
unlikely to reach the site of the former barrier until Barrier 1 is modified for fish passage.
The barrier was a perched culvert associated with an unpaved road that prevented upstream fish passage
due to its height above the stream bed. The culvert was removed and replaced with a three-sided free-span
bridge. The stream was re-graded with a boulder step pool sequence. The RCD and landowner selected
these recommended alternatives after field surveys as well as discussions and site visits with
representatives of the National Marine Fisheries Service (NMFS), CDFG, RWQCB, and the PCAC (RCD
2007b). However, based upon assessments in November 2007 (Alley 2007bA) of similar structures
installed in 1997-1998 on Mills Creek and Arroyo Leon, the boulder weirs are likely to fail during large
storms. Boulders will probably move, leaving gaps in the weirs, and down-cutting will probably occur at
the downstream weir, because of the sandy channel bed and banks. Grouting the boulders together may be
necessary to prevent or correct failures after boulders move. Additional weirs may be required
downstream of the recent project to remediate future down-cutting.
The RCD sought additional funds from the City of San Mateo Wastewater Treatment Plan (SMWTP) to
meet the construction and permitting costs which have increased since the inception of the project.

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SMWTP awarded the funds to the RCD, who will continue to be responsible for managing the Apanolio
Canyon Fish Passage Enhancement Project including all compliance schedules set forth by the RWQCB.
Plans have been developed for barriers 1 and 2, but no funds are presently available for implementation
and new permits for modifying the barriers are required.
7.5 INSTALL VORTEX WEIRS ON PILARCITOS CREEK
Water Resources Engineering Company (WRECO) is designing a fish passage restoration at Pilarcitos
Creek in San Mateo County as a part of an ongoing Hydraulic On-call Services to CalTrans District 4
(WRECO 2007). The fish passage project is required for the mitigation of two CalTrans Highway 92
improvement projects. The proposed project will remove a 5-foot concrete drop structure at Highway 92
and replace it by 5-step rock vortex weirs. The design efforts were coordinated with NMFS and CDFG.
The original proposal in PWA (1996) was to install some vortex weirs as a test to see if they could be
used to provide improved pool habitat. However, because of the high expense and failure rate of
ungrouted weirs used for passage improvement in the sandy channel beds of the watershed (Alley
2007bA), no use of boulder weirs for rearing habitat improvement seems desirable.
7.6 INCREASE INSTREAM FLOW TO ESTUARY
Additional summer stream flow for lower Pilarcitos Creek and the lagoon may require either the use of
reclaimed wastewater or the substitution of reclaimed waste water for stream diversions or well use. No
feasibility studies have been done. When the Pilarcitos Creek lagoon configuration is pushed far to the
north, Frenchman’s Creek also discharges to the lagoon. Like most small lagoons on the central coast,
there is almost no residual depth in the Pilarcitos Creek lagoon when the sandbar is open. When the
sandbar is closed sufficient inflows (in excess of sandbar seepage) are needed to raise the lagoon level to
provide usable habitat for steelhead rearing.
7.7 FISH BARRIER MODIFICATION OR REMOVAL ON ARROYO LEON
PWA (1996) noted 3 barriers on Arroyo Leon (2 large on-channel dams and a severe culvert barrier).
7.7.1 Severe Culvert Barrier
The barrier on Arroyo Leon upstream of the mouth of Mills Creek was a drop at a failed culvert/road
crossing. It was modified in 1997 with a bridge and a series of boulder weirs/step pools. The step pools
provided access to Arroyo Leon upstream of Mills Creek. An assessment in November 2007 (Alley
2007bA) found that boulders within the downstream weir had moved, and channel down-cutting had
occurred at the lower weir. Presently, fish passage by upstream migrating adult steelhead is likely
restricted to higher winter flows of 50-75+ cfs. However, unless the boulders are grouted together,
additional boulder movement is likely to occur. The channel down-cutting in the sandy bed and banked

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channel may require installation of another weir (any additional weir may also result in down-cutting).
Only one weir (under the driveway bridge) was visible in 2007; the others were apparently buried under
sand from an eroding hillslope and attempted bank repair on the right (north bank), upstream of the
bridge.
7.7.2 Johnson Ranch (“Giusti Farms”) Dams and On-Channel Ponds
The Restoration Plan (PWA, 1996) report recognized that steelhead rearing of unknown extent took place
in these 2 on-channel seasonal ponds operated for agricultural water supply. The ponds are on land owned
by the Pennisula Open Space Trust (POST) and leased to Guisti Farms for agricultural use. Several
potential problems with operation were suspected. First, in spring, when steelhead smolts were migrating
downstream, the ponds could block migration by: 1) early installation (prior to June); 2) not providing for
fish passage over the dams (a thin sheet of water over the spillway); and 3) not providing adequate bypass
flows for passage downstream of the dams during filling and subsequent operation. In addition, the old
slide gates that closed the dams could not be opened until most of the water had been drained from the
reservoirs; draining through the small pipes near the bottom could take 2-3 or more weeks to drain. This
meant that after the irrigation season was over (late October) the reservoirs were regularly drained down
and opened, so that the first big rains did not occur with inoperable reservoir gates. These actions would
often drain the ponds (and stop rearing) prior to sufficient rains to sustain flows downstream of the dams
and could result in killing many of the fish reared in the ponds in some years. Finally, although the ponds
were regularly illegally fished for “catchable-sized” trout, the population size and growth rates of
steelhead in the ponds were unknown and might be affected by high water temperatures or dissolved
oxygen problems in the ponds.
In 2000 and 2001 installation of the dams was delayed until mid May and passage over the upper dam
was provided (notched weir) under restrictions in a CDFG streambed alteration agreement. The lower
dam was closed about 2 weeks later, but no downstream fish passage was provided at the lower dam
(after late May) in either year because the reservoir never filled to the point of spilling. Studies of the
ponds (Smith 2001 and 2002) showed that relatively few smolts (2 year olds) from the upper watershed
were apparently trapped by the closure. Studies also showed that large numbers (estimated at 1984 fish in
2000) of fast-growing young-of-year and yearling steelhead reared in the 2 ponds in both years.
The ponds were often over 5 m deep and stratified with warmer water on/near the surface and cooler
water below, and with lower dissolved oxygen levels in the lower half of the water column. Water
temperatures (based upon temperature array recorders and periodic water column profiles) were generally
cool (< 20 degrees C) in the upper pond, but surface temperatures were often higher in the lower pond
(22-24 degrees C). Temperature and dissolved oxygen conditions in the ponds were driven by weather
(sunny versus overcast days) rather than by seasonal changes from June to September. Overcast days
brought cooler water but reduced oxygen concentrations. Since algae (phytoplankton and filamentous)
were common in the ponds, dissolved oxygen levels declined due to plant respiration and limited
photosynthesis during persistent overcast periods.

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In the second year water fern (Azolla) coated much of the surface of the lower pond in late summer,
reducing wind-driven mixing and reducing water column dissolved oxygen. Despite some water quality
problems, the steelhead that reared in the ponds showed very high growth rates and the fish in the lower
pond (with warmer water in both years and some dissolved oxygen problems in 2001) were larger than
those in the upper pond in both years. Young-of-year fish in the ponds were generally much larger by fall
than yearlings produced in 2 years of rearing in upstream habitats, and yearlings rearing in the ponds
during their second year were 150-250+ mm standard length (6-10 inches long) by November.
Conditions in the ponds were similar to the warmer, but highly productive, conditions that provide for
rearing large smolt-sized fish in lagoons at the mouths of many central coast streams (Smith 1990; Bond
2006; Alley 2007bd). In addition, the studies by Bond (2006) demonstrated that the very large fish
produced in Scott Creek lagoon (similar to the sizes in the Guisti ponds) made up a disproportionately
large portion of the returning adults in that watershed, because smaller smolts rearing in upstream habitats
had very low ocean survival. In Arroyo Leon, the ponds in both years produced more than 10 times the
smolts as an equivalent amount of stream habitat (based upon sampling in the shaded, sandy, low-flow
habitat upstream of the ponds) (Smith 2001 and 2002). In addition, because of their larger size and much
higher likelihood of ocean survival (Bond 2006), the number of returning adults produced by the ponds
was probably 100 times that of an equivalent length of Arroyo Leon stream habitat (and may have
accounted for a majority of returning adult steelhead in the entire Pilarcitos watershed).
Preliminary (concept) plans were developed for modifying the dams (with new slide gates and drainage
valves) to allow bypass flows during filling, fish passage over full ponds, and to allow rapid draining
immediately prior (or during) the first large rains in fall (or winter). These modifications would eliminate
most of the fish passage and other problems associated with operation of the ponds. However, the ponds
have not been used since 2001 due to lack of a streambed alteration agreement with the CDFG and a
decision by NMFS that “take” (adverse effects) on steelhead at the dams/ponds required an “incidental
take agreement” (either a section 7/consultation (if a federal nexus was involved) or section 10/Habitat
Conservation Plan) that demonstrated a net beneficial effect on steelhead of operating the ponds. In the
years since the ponds have ceased operation, few steelhead have apparently reared at the site of the ponds,
since the streambed is normally dry or intermittent by September of all but the wettest years ( Tim Frahm
and Keith Mangold, pers. comm.).
Although operating one or both of the ponds in a “fish-friendly” manner is preferable for watershed
steelhead production, because of the regulatory restrictions on the use of the ponds, POST is developing a
feasibility study to remove the two impoundments. Agricultural land owners have relied on the reservoirs
created behind these impoundments for irrigation during the dry season and are now faced with water
supply losses that in many cases will put them out of business. POST aims to develop a solution that
replaces the ponds with in-stream habitat and provides an agricultural water supply. The solution will
replace the ponds with approximately 1/2 mile of typically non-perennial, low quality stream habitat,

12/28/07 71
eliminate any restriction by the dams to in-stream spawning and rearing habitat above the dams, and
provide a long-term off-stream supply of water for irrigation.

12/28/07 72
8. REFERENCES
Albion Environmental. 1998. San Francisco Bay Area Ridge Trail Marbled Murrelet and Spotted Owl
survey findings.
Alley, D. W. 2007a. Apanolio Creek fishery assessment December. Prepared for this project.
Alley, D. W. 2007b. Comparisons of 2006 juvenile steelhead densities in drainages of the San Lorenzo,
Soquel, Aptos and Corralitos watersheds in Santa Cruz County, California. Prepared for Santa
Cruz County Environmental Health Department.
Alley, D. W. 2007c. Evaluation of present condition of past fish passage improvement projects on Arroyo
Leon and Mills Creeks. Prepared for this project.
Alley, D.W. 2007d. Soquel Creek Lagoon Monitoring Report, 2006. Prepared for the City of Capitola.
Avocet Research Associates. 2005. Protocol-level surveys for Marbled Murrelet (Brachyrampus
marmoratus marmoratus) at Cahill Ridge and the Upper Pilarcitos Creek Watershed San Mateo
County, California: 2005. Prepared for Tetra Tech, Inc. and the San Francisco Public Utilities
Commission.
Avocet Research Associates. 2006. Protocol-level surveys for Marbled Murrelet (Brachyrampus
marmoratus marmoratus) at Cahill Ridge and the Upper Pilarcitos Creek Watershed San Mateo
County, California: 2006. Prepared for the San Francisco Public Utilities Commission.
Balance (Balance Hydrologics, Inc.) (with Schaaf & Wheeler and EIP Associates). 1997. Pilarcitos Creek
alternative point of CCWD diversion study. Prepared for Coastside County Water District.
Balance (Balance Hydrologics, Inc.). 2001. Sediment-Transport Reconnaissance of the Pilarcitos Creek
Watershed, San Mateo County, California – Water Year 2000. Prepared for Pilarcitos Creek
Advisory Committee and San Mateo County Resource Conservation District.
Balance (Balance Hydrologics, Inc.). 2003a. Hydrologic analysis of streamflow parameters for Arroyo
Leon at Giusti Farm: Half Moon Bay, San Mateo County, California. Prepared for EDAW, Hagar
Environmental Science, and Peninsula Open Space Trust.
Balance (Balance Hydrologics, Inc.). 2003b. Catalog of Active Sediment Sources and Control
Opportunities, Apanolio Creek, Half Moon Bay, San Mateo County, California. Prepared for San
Mateo County Resource Conservation District, Pilarcitos Creek Advisory Committee.
Bell, D.T. and Williams, J.E. 1997. Eucalypt ecophysiology. In: J.E. Williams and J.C.Z. Woinarski
(Editors), Eucalpytus ecology: individuals to ecosystems. The Press Syndicate of the University
of Cambridge, Cambridge, UK, pp. 168-196.

12/28/07 73
Benda, L. E. and T. W. Cundy. 1990. "Predicting deposition of debris flows in mountain channels."
Canada Geotechnical Journal 27: 409-417.
Bond, M. H. 2006. The importance of estuarine rearing to Central California steelhead (Oncorhynchus
mykiss) growth and marine survival. M. A. Thesis. University of California, Santa Cruz.
Brabb, E.E. et al. 1998. Geology of the onshore part of San Mateo County, California: A Digital
Database. Derived from USGS Pamphlet OF98-137.
CCC (California Coastal Conservancy). 2006. Frenchman’s Creek Fish Passage File No. 06-033. Project
Manager Janet Diehl.
CCWD (Coastside County Water District). 2006. Water Supply Evaluation Report Calendar Year 2005,
March.
CDM and Merritt Smith Consulting. 2003a. San Francisco garter snake and red-legged frog survey report
and Marbled Murrelet survey report. Prepared for the San Francisco Public Utilities Commission.
CDM and Merritt Smith Consulting. 2003b. Marbled Murrelet monitoring plan. Prepared for the San
Francisco Public Utilities Commission.
CNDDB (California Natural Diversity Database). 2007. Rarefind. California Department of Fish and
Game.
CNPS (California Native Plant Society). 2007. Inventory of Rare and Endangered Plants of California (6th
edition). Rare Plant Scientific Advisory Committee, David P. Tibor, Convening Editor.
http://cnps.web.aplus.net/cgi-bin/inv/inventory.cgi
CWHR (California Wildlife Habitat Relationships System). 2005. Geographic Information Systems
Shape Files of Vegetation Types. Prepared by the California Department of Fish and Game and
California Interagency Wildlife Task Group.
DEP (Department of Environmental Management), San Mateo County, California. 1986. General Plan.
Dietrich, W. E., S. L. Reneau, et al. 1987. Overview: "Zero-order basins" and problems of drainage
density, sediment transport and hillslope morphology. Erosion and Sedimentation in the Pacific
Rim, Corvallis, OR, IAHS.
Dietrich, W. E., and Dunne, T. 1978. "Sediment Budget for a small catchment in mountainous terrain."
Zeitschrift Für Geomorphologie 29: 191-206.
Doerr, S.H. 1998. On standardizing the ‘water drop penetration time’ and the ‘molarity of an ethanol
droplet’ techniques to classify soil hydrophobicity: a case study using medium textured soils.
Earth Surface Processes and Landforms 23: 663-668.

12/28/07 74
Doerr, S.H. et al. 2005. Effects of contrasting wildfire severity on soil wettability in Australian eucalypt
catchments. Journal of Hydrology In Press.
EDAW, Inc. et al. 2002. Peninsula Watershed Management Plan. Prepared for the San Francisco Public
Utilities Commission.
Ellen, S.D., Mark, R.K., Wieczorek, G.F., Wentworth, C.M., Ramsey, D.W., and May, T.E. 1997. Map
Showing Principal Debris-Flow Source Areas in the San Francisco Bay Region, California. US
Geological Survey Open File Report 97-745e. 8pp.
Environmental Services Agency – County of San Mateo (ESA-SM). 1998. Local Coastal Program.
ENTRIX. 2006a. Pilarcitos Creek aquatic habitat and fish population survey, September 2004. Prepared
for City of San Francisco Public Utilities Commission. Appendix A in Kennedy/Jenks
Consultants 2006. Final Pilarcitos Operations Report. Prepared for San Francisco Public Utilities
Commission.
ENTRIX. 2006b. Evaluation of flow-habitat relationships in Pilarcitos Creek downstream of Stone Dam.
Prepared for City of San Francisco Public Utilities Commission. Appendix B in Kennedy/Jenks
Consultants 2006. Final Pilarcitos Operations Report. Prepared for San Francisco Public Utilities
Commission.
EOA. 1990. Country of San Mateo Feasibility Study for the Pilarcitos Creek Watershed Restoration
Program.
Ferriera, A.J.D. et al. 2000. Hydrological implications of soil water-repellency in Eucalyptus globulus
forests, north-central Portugal. Journal of Hydrology 231-232: 165-177.
Flosi, G. et al. 1998. California Salmonid Stream Habitat Restoration Manual, 3rd Edition. CA
Department of Fish and Game, Inland Fisheries Division.
Frahm, Tim. 2002-2007. Personal Communication. Pilarcitos watershed resident and stakeholder.
Freeman, J.R.. 1912. The Hetch Hetchy Water Supply for San Francisco. Prepared for James Rolph, Jr.,
Mayor of San Francisco and Percy V. Long, City Attorney.
Go Native Nursery LLC. 2002. Johnson Ranch/Arroyo Leon Vegetation Survey. Prepared for the
Peninsula Open Space Trust.
HTB (Heal the Bay). 2004. 14th Annual Beach Report Card for 2003-2004.
HTB (Heal the Bay). 2007. 17th Annual Beach Report Card for 2006-2007.

12/28/07 75
Leighton-Boyce, G. et al. 2005. Temporal dynamics of water repellency and soil moisture in eucalyptus
plantations, Portugal. Australian Journal of Soil Research 43(3): 269-280.
Kennedy/Jenks Consultants. 2006. Final Pilarcitos Operations Report. Prepared for San Francisco Public
Utilities Commission.
Mangold, Keith. 2002-2007. Personal Communication. Pilarcitos watershed resident and stakeholder.
Marston, D. 1993. Sediment assessment report. Pilarcitos Creek, San Mateo County. CDFG Report,
January.
Montgomery and Buffington. 1997. Channel-reach morphology in mountain drainage basins. Geological
Society of America Bulletin. 109: 596-611.
Natural Resources Conservation Service, United States Department of Agriculture (SSURGO). Soil
Survey Geographic Database). For San Mateo County, California
[http://soildatamart.nrcs.usda.gov]
NCDC (National Climatic Data Center). 2007. Western Regional Climate Center archive for the Half
Moon Bay National Weather Service Station Report 043714-4.
Nelson, E.A. 1997. Phase I of Lower Pilarcitos Creek Groundwater Investigation, Half Moon Bay,
California. Prepared for the Coastside County Water District.
Nelson, E.A. 1998. Phase II of Lower Pilarcitos Creek Groundwater Investigation, Half Moon Bay,
California. Prepared for the Coastside County Water District.
Pryor, L.D. 1976. The biology of eucalypts. Edward Arnold United, London, UK.
PWA (Philip Williams & Associates, Ltd.) (with Habitat Restoration Group, Prunuske Chatham and
Callander Associates). 1996. Pilarcitos Creek Restoration Plan. Prepared for Regional Water
Quality Control Board and California Department of Fish and Game. Report no. 1021.
Ralph, C.J., G.L.Hunt, M. G. Raphael, and J. F. Piatt. 1995. Ecology and Conservation of the Marbled
Murrelet. USDA Forest Service Gen. Tech. Rep. PSW-152. 1995.
Ramirez, Tim. 2007. Personal Communication. SFPUC staffmember. Pilarcitos IWMP Workgroup
Meeting May 9.
RCD (San Mateo County Resource Conservation District). 2007a. Apanolio Canyon Fish Passage
Enhancement Project – Project Description. [http://www.swrcb.ca.gov/rwqcb2/Agenda/04-11-
07/6/SEP%20San%20Mateo.pdf]

12/28/07 76
RCD (San Mateo County Resource Conservation District). 2007b. Memorandum of Understanding
January 25.
RWQCB (Regional Water Quality Control Board), San Franciso Region. 2006. Order no. R2-2006-0040:
Updated Waste Discharge Requirements for Browning-Ferris Industries, Inc., Ox Mountain Class
III Waste Management Facility, Half Moon Bay, San Mateo County.
Sciaromi, Hank. 2007. Personal Communication. Operates nursery along Pilarcitos Creek.
Scott, D.F. and Lesch, W. 1997. Streamflow responses to afforestation with Eucalyptus grandis and Pinus
patula and to felling in the Mokobulaan experimental catchments, South Africa. Journal of
Hydrology 199: 360-377.
Sequoia Audubon Society. 2001. San Mateo County Breeding Bird Atlas.
Seymour R. and M. Westphal. 2000. Results of a one-year survey for amphibians on lands managed by
the Midpenisula Regional Open Space District in the Santa Cruz Mountains of California.
Prepared for Midpenisula Regional Open Space District.
Shakesby, R.A., Doerr, S.H. and Walsh, R.P.D. 2000. The erosional impact of soil hydrophobicity:
current problems and future research directions. Journal of Hydrology 231-232: 178-191.
Smith, Jerry, 2007. Personal Communication. Fisheries biologist and member of the consultant team.
Smith, J. J. 1996. Appendix C: 1996 evaluations for Arroyo Leon and upper Pilarcitos Creek.
Smith, J. J. 1998. The effect of the CalTrans project to remove gabions and repair the Highway 92 road
culvert upon habitat and fisheries of Albert Canyon. Report to CalTrans.
Smith, J. J. 1999. Steelhead abundance in Albert Canyon and Pilarcitos Creek upstream and downstream
of Highway 92 in November 1999. Report to CalTrans.
Smith, J. J. 1990. The effects of sandbar formation and inflow on aquatic habitat and fish utilization in
Pescadero, San Gregorio, Waddell and Pomponio creek estuary/lagoon systems 1985-1989.
Report to California Department of Parks and Recreation.
Smith, J. J. 2001. Progress report: 2000 studies of habitat conditions and steelhead in the Arroyo Leon
seasonal reservoirs.
Smith, J. J. 2002. Habitat conditions and steelhead in the Arroyo Leon seasonal reservoirs and adjacent
stream in 2001.
Smith, J. J. 2006. Distribution and abundance of juvenile coho and steelhead in Gazos, Waddell and Scott
creeks in 2006.

12/28/07 77
Smith, J.J. and H.W. Li. 1983. Energetic factors influencing foraging tactics of juvenile steelhead trout
Salmo gairdneri. D.L.G. Noakes, et al. (eds.). Predators and Prey in Fishes. Dr. W. Junk
Publishers, the Hague. pp. 173-180.
Suddjian, D. 2007. Personal Communication. Biologist.
Swaim Biological. 2006. Results of the 2005 surveys for the San Francisco garter snake and California
red-legged frog at Mud Dam 1, Mud Dam 2, Skyline Quarry, and Stone Dam San Mateo County,
California. Report to Tetra Tech.
Teter. J. 2002. Preliminary Report on Estimated Cost of Water Production from the Proposed Lower
Pilarcitos Creek Groundwater Project.
Thompson, A. 2006. Soil Water Repellency and Eucalyptus globulus in Coastal California. San Francisco
State University, pp. 20.
Todd Engineers. 2003. Lower Pilarcitos Creek Groundwater Basin Study. Prepared for the Coastside
County Water District.
Trihey and Associates. 1995. An assessment of habitat conditions for juvenile trout in the portion of
Pilarcitos Creek on CCWD property. Prepared for Coastside County Water District.
Trihey and Associates. 1996. Fishery survey on Pilarcitos Creek. Prepared for San Francisco Water
Department.
URS Corporation. 2004. Peninsula watershed Marbled Murrelet survey report. Prepared for the San
Francisco Public Utilities Commission.
US Interagency Advisory Committee on Water Data. 1982. Guidelines for determining flood flow
frequency, Bulletin 17-B of the Hydrology Subcommittee: Reston, Virginia, U.S. Geological
Survey, Office of Water Data Coordination, [183 pp.]. [Available from National Technical
Information Service, Springfield VA 22161 as report no. PB 86 157 278 or from FEMA on the
World-Wide Web at http://www.fema.gov/mit/tsd/dl_flow.htm.]
USDA (US Department of Agriculture) National Agriculture Imagery Project (NAIP). 2006.
[http://datagateway.nrcs.usda.gov/GatewayHome.html]
USFWS (US Fish and Wildlife Service). 1992. Endangered and Threatened Wildlife and Plants;
Determination of Threatened Status for the Washington, Oregon, and California Population of the
Marbled Murrelet. Federal Register 57(191):45328-45337.
USFWS (US Fish and Wildlife Service). 1996. Endangered and Threatened Wildlife and Plants; Final
Designation of Critical Habitat for the Marbled Murrelet. Federal Register 61(102):26256-26320.

12/28/07 78
USFWS (US Fish and Wildlife Service). 2006. Endangered and Threatened Wildlife and Plants;
Designation of Critical Habitat for the Marbled Murrelet. Federal Register 71(176):53838-53951.
WRECO ( Water Resources Engineering Company). 2007. Project description for Pilarcitos Creek Fish
Passage Restoration Project. [http://www.wreco.com/projects/restoration/coastal.html#pilarcitos]
Zatkin, R. 2002. San Mateo County Coastal Streams, Apanolio Creek, Arroyo Leon, Corinda Los
Trancos, Mills Creek, Nuff Creek, Pilarcitos Creek. A compendium of information from the
California Department of Fish and Game, two volume manuscript at Water Resources Center
Archives.

12/28/07 79
9. LIST OF PREPARERS
This report was prepared by the following PWA staff:
Adam Parris, Project Manager

Setenay Bozkurt, Fluvial Geomorphologist
Elizabeth Andrews, PE, Project Director
Catherine Lee, Production Manager
With:
Mike Liquori, Senior Plan Writer/Geomorphologist, Sound Watershed Consulting

Max Busnardo, Restoration Ecologist, H. T. Harvey and Associates
Matthew Ramsay, Restoration Ecologist, H. T. Harvey and Associates
Don Alley, Fisheries Biologist, D.W. ALLEY & Associates
Jerry Smith, PhD, Fisheries Biologist, D.W. ALLEY & Associates
Joe Hayes, Hydrogeologist, Weber-Hayes and Associates

12/28/07 80
10. FIGURES
Figure 1. Pilarcitos Drainage Network

Figure 2. Mean Annual Rainfall in the Pilarcitos Watershed
Figure 3. Total Annual Precipitation at Half Moon Bay
Figure 4. Total Annual Precipitation at Pilarcitos Dam
Figure 5. Median Monthly Precipitation Variation at Half Moon Bay
Figure 6. Daily Precipitation Variation at Pilarcitos Dam
Figure 7. Pilarcitos Streamflow at Half Moon Bay
Figure 8. Total Annual Discharge from Pilarcitos Creek at Half Moon Bay
Figure 9. Annual Hydrograph for Pilarcitos Creek at Half Moon Bay
Figure 10. Peak Instantaneous Discharge at Half Moon Bay
Figure 11. Peak Annual Discharge (Log Pearson III)
Figure 12. Annual Days with Zero Recorded Flow at Half Moon Bay
Figure 13. Rating Curve for Pilarcitos Creek near Half Moon Bay
Figure 14. Rating Curve Shift Adjustment for Pilarcitos Creek near Half Moon Bay
Figure 15. Pilarcitos Streamflow at Stone Dam
Figure 16. Annual Hydrograph for Pilarcitos Creek below Stone Dam
Figure 17. Rating Curve for Pilarcitos Creek below Stone Dam
Figure 18. Streamflow Gain Between Stone Dam and Half Moon Bay
Figure 19. Proportion of Flow from Lower Watershed
Figure 20. Annual Flow Exceedance Pilarcitos at Half Moon Bay
Figure 21. Water Supply Network
Figure 22. Water Diversions from 1996 to 2007
Figure 23. Geologic Units and Surface Deposits
Figure 24. Soil Particle Size
Figure 25. Hillslope Failure and Channel Erosion
Figure 26. Channel Grade Summary
Figure 27. Watershed Slope
Figure 28. Partial Road Map
Figure 29. Stream Gradient in the Pilarcitos Watershed
Figure 30. Annual Peak Discharge Probability Pilarcitos Creek at HMB
Figure 31. California Wildlife Habitat Relationship (CWHR) Vegetation Data
Figure 32. Locations of Riparian Plant Communities and Eucalyptus Groves (South)
Figure 33. Locations of Riparian Plant Communities and Eucalyptus Groves (North)
Figure 34. Locations of Significant Concentrations of Invasive, Non-native Plant Species (South)
Figure 35. Locations of Significant Concentrations of Invasive, Non-native Plant Species (North)
Figure 36. Vegetation Communities
Figure 37. California Natural Diversity Database (CNDDB) Plant Records
Figure 38. California Natural Diversity Database (CNDDB) Animal Records
Figure 39. Marbled Murrelet Habitat / Occurrences

12/28/07 81
Project Location
e l
nn
Tu
s
lar
Pi
Stone Dam
Skyline Quarry
Nu
Co rri nd a Lo
ff C Upper Crystal Springs Reservoir

re e
Alb
k
e
rt C
s Tr
any
an
Ap
on
co
no
a
s
lio
Cree
k
ek
re
k
sC
ee
c ito
Cr
ar
na
Pi l
M ad o n
k
C ree
ls
l
Mi

Headwater Drainage
Second Order
Third Order
n
o
Le
Fourth Order (Tributary)

Ar r o yo
Fifth Order (Perrennial)

Note: Headwater drainage is defined as a first order stream. figure 1
Drainage area for this class ranges from approximately 20 - 80 acres.
±
Pilarcitos IWMP
0 0.5 1 2
\\Sfo1\GIS\Pilarcitos\Figures\DrainageNetwork.mxd
#
Existing Gauge Locations
# rain gauge, existing
" reservoir stage gauge, existing
(
! stream gauge, existing
Mean Annual Rainfall (in)
27 - 30
31 - 35
" # 36 - 45
Upper Pilarcitos
"
(
!
Apanolio
Nuff Creek
Corrinda Los Trancos #

Albert Canyon
Middle Pilarcitos
Madonna Creek
Lower Pilarcitos
(
!
Mills Creek
Lower Arroyo Leon
Upper Arroyo Leon
Source: USGS (quadrangle, dem), USDA (rainfall PRISM,2005),

figure 2
±
SPUC (water bodies, gauges locations)
Pilarcitos IWMP
Mean Annual Rainfall in the Pilarcitos Watershed
0 0.5 1 2
\\Sfo1\GIS\Pilarcitos\Pilarcitos_MAP.mxd
Total Annual Preciptiation
60
50
Delete this Paragraph and Insert Image Here
40
Annual Precipitation (in)
30
20
10
0
1948
1950
1952
1954
1956
1958
1960
1962
1964
1966
1968
1970
1972
1974
1976
1978
1980
1982
1984
1986
1988
1990
1992
1994
1996
1998
2000
2002
2004
2006
Notes: National Weather Service via Western Regional Climate Center.
Source: Sound Watershed Consulting fi gure 3
Pilarcitos IWMP
Total Annual Precipitation at Half Moon Bay
PWA Ref# 1884-T3A
P:\Projects\1884_Pilarcitos IWMP\Task3A_AssessmentUpdate\Figures\HMB pptV2.doc

Daily Precipitation at Pilarcitos Dam
7.00
6.00
5.00
Daily Precipitation (in)
4.00
3.00
2.00
1.00
0.00
1909
1912
1915
1918
1921
1924
1927
1930
1933
1936
1939
1942
1945
1948
1951
1954
1957
1960
1963
1966
1969
1972
1975
1978
1981
1984
1987
1990
1993
1996
Notes: SFPUC
Pilarcitos IWMP
Total Annual Precipitation at Pilarcitos Dam
PWA Ref# 1884-T3A
P:\Projects\1884_Pilarcitos IWMP\Task3A_AssessmentUpdate\Figures\PD ppt V2.doc

Monthly Precipitation at Half Moon Bay
9.0

8.0
7.0
Monthly Precipitation (in)
6.0
5.0
4.0
3.0
2.0
1.0
0.0
JAN FEB MAR APR MAY JUN JUL AUG SEP OCT NOV DEC
Notes: National Weather Service. Error bars represent the 25th and 75th percentile of the monthly precipitation distribution. Total
length of record = 54-58 years. fi gure 5
Source: Sound Watershed Consulting Pilarcitos IWMP
Median Monthly Precipitation Variation at Half Moon
Bay
PWA Ref# 1884-T3A
P:\Projects\1884_Pilarcitos IWMP\Task3A_AssessmentUpdate\Figures\HMB ppt varV2.doc

Daily Precip Record
Pilarcitos Dam
7
Max
Avg
6
5
Daily Precipitation (in)
0
1-Jan 20-Feb 10-Apr 30-May 19-Jul 7-Sep 27-Oct 16-Dec
Notes: SFPUC
Pilarcitos IWMP
Daily Precipitation Variation at Pilarcitos Dam
PWA Ref# 1884-T3A
P:\Projects\1884_Pilarcitos IWMP\Task3A_AssessmentUpdate\Figures\PD ppt var V2.doc

Pilarcitos at Half Moon Bay
2500
2000
Discharge (cfs)
1500
1000
500
0
May-66 Nov-71 May-77 Oct-82 Apr-88 Oct-93 Mar-99 Sep-04
Notes: USGS Station (11162630)

Source: Sound Watershed Consulting
fi gure 7
Pilarcitos IWMP
Pilarcitos Streamflow at Half Moon Bay
PWA Ref# 1884-T3A
P:\Projects\1884_Pilarcitos IWMP\Task3A_AssessmentUpdate\Figures\Pilarcitos Streamflow V2.doc

Total Annual Discharge at Half Moon Bay
60,000
50,000
40,000
Discharge (ac-ft) .
30,000
20,000
10,000
0
1966/7
1967/8
1968/9
1969/7
1970/1
1971/2
1972/3
1973/4
1974/5
1975/6
1976/7
1977/8
1978/9
1979/8
1980/1
1981/2
1982/3
1983/4
1984/5
1985/6
1986/7
1987/8
1988/9
1989/9
1990/1
1991/2
1992/3
1993/4
1994/5
1995/6
1996/7
1997/8
1998/9
1999/0
2000/1
2001/2
2002/3
2003/4
2004/5
2005/6
Notes:
Pilarcitos IWMP
Total Annual Discharge from Pilarcitos Creek at Half
Moon Bay
PWA Ref# 1884-T3A
P:\Projects\1884_Pilarcitos IWMP\Task3A_AssessmentUpdate\Figures\Pilarcitos Annual Q V2.doc

100
25th Percentile
Median
90
75th Percentile
80
70
Discharge (cfs) .
60
50
40
30
20
10
0
6-Aug 25-Sep 14-Nov 3-Jan 22-Feb 12-Apr 1-Jun 21-Jul 9-Sep 29-Oct
Date
Notes: Annual hydrograph represents the typical conditions over the period of record. Flows below the 25th percentile typically
indicate drought periods, while flows above the 75th percentile are typically considered unusually wet years. fi gure 9
Annual Hydrograph for Pilarcitos Creek at Half Moon
Bay
PWA Ref# 1884-T3A
P:\Projects\1884_Pilarcitos IWMP\Task3A_AssessmentUpdate\Figures\Pilarcitos Hydrograph at HMB V2.doc

Peak Instantaneous Discharge
5000
4500
4000
3500
3000
Discharge (cfs)
2500
2000
1500
1000
500
0
1967
1968
1969
1970
1971
1972
1973
1974
1975
1976
1977
1978
1979
1980
1981
1982
1983
1984
1985
1986
1987
1988
1989
1990
1991
1992
1993
1994
1995
1996
1997
1998
1999
2000
2001
2002
2003
2004
2005
2006
Notes:
Source: Sound Watershed Consulting f i g u r e 10
Pilarcitos IWMP
Peak Instantaneous Discharge at Half Moon Bay
PWA Ref# 1884-T3A
P:\Projects\1884_Pilarcitos IWMP\Task3A_AssessmentUpdate\Figures\PeakQ_2 V2.doc

Annual Peak Discharge Probability
Pilarcitos Creek at Half Moon Bay
5000
4500
Peak Discharge (cfs

4000
3500
3000
2500
2000
1500
1000
500
0
1 0.1 0.01
Exceedence Probability Exceedence
(log scale) 95% Confidence Interval
Weibull
Notes:
Pilarcitos IWMP
Peak Annual Discharge (Log Pearson III)
PWA Ref# 1884-T3A
P:\Projects\1884_Pilarcitos IWMP\Task3A_AssessmentUpdate\Figures\PeakQ V2.doc

Total Days of No Discharge
300
250
200
.
# of Days
150
100
50
0
1966/7
1967/8
1968/9
1969/7
1970/1
1971/2
1972/3
1973/4
1974/5
1975/6
1976/7
1977/8
1978/9
1979/8
1980/1
1981/2
1982/3
1983/4
1984/5
1985/6
1986/7
1987/8
1988/9
1989/9
1990/1
1991/2
1992/3
1993/4
1994/5
1995/6
1996/7
1997/8
1998/9
1999/0
2000/1
2001/2
2002/3
2003/4
2004/5
2005/6
Notes:
Pilarcitos IWMP
Annual Days with Zero Recorded Flow at Half Moon Bay
PWA Ref# 1884-T3A
P:\Projects\1884_Pilarcitos IWMP\Task3A_AssessmentUpdate\Figures\Pilarcitos No Flow V2.doc

14
12
10
Gage Height (ft)
0
0 500 1000 1500 2000 2500 3000 3500 4000 4500 5000
Peak Discharge (cfs)
Source: Sound Watershed Consulting

f i g u r e 13
Pilarcitos IWMP
Rating Curve for Pilarcitos Creek near Half Moon

Bay
PWA Ref# 1884-T3A
P:\Projects\1884_Pilarcitos IWMP\Task3A_AssessmentUpdate\Figures\rating V2.doc

Cumulative Rating Curve Shift Adjustment
3.00
2.00
1.00
0.00
Rating Adjustment (ft)
-1.00
-2.00
-3.00
-4.00
-5.00
-6.00
-7.00
Oct-87 Jul-90 Apr-93 Jan-96 Oct-98 Jul-01 Apr-04 Dec-06
Date
Notes: USGS station (11162630) measurement data. Plot indicates channel changes near the gage location that
influence gage
f i g u r e 14
Rating Curve shift Adjustment for Pilarcitos Creek near
Half Moon Bay
PWA Ref# 1884-T3A
P:\Projects\1884_Pilarcitos IWMP\Task3A_AssessmentUpdate\Figures\rating adjustment V2.doc

Pilarcitos below Stone Dam
200
180
160
140
Discharge (cfs)
120
100
80
60
40
20
0
Oct-97 Feb-99 Jun-00 Nov-01 Mar-03 Aug-04 Dec-05 May-07
Notes: USGS station (11162620)

Pilarcitos IWMP
Pilarcitos Streamflow at Stone Dam
PWA Ref# 1884-T3A
P:\Projects\1884_Pilarcitos IWMP\Task3A_AssessmentUpdate\Figures\Pilarcitos Streamflow at Stone Dam V2.doc

Pilarcitos Below Stone Dam
40
25th Percentile
Median
35 75th Percentile
30
25
.
Discharge (cfs)
20
15
10
0
Date
Notes:
Pilarcitos IWMP
Annual Hydrograph for Pilarcitos Creek below Stone Dam
PWA Ref# 1884-T3A
P:\Projects\1884_Pilarcitos IWMP\Task3A_AssessmentUpdate\Figures\Pilarcitos Hydrograph at StoneDam V2.doc

Rating
Rating Curve
Pilarcitos Creek below Stone Dam
50
300
45
2
y = 51.644x - 58.989x + 19.52
250
R2 = 0.961
40
200
35
150
Discharge (cfs)
30 100
25 50
0
20 1.5 2.0 2.5 3.0
15
10
0
0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 1.1 1.2 1.3 1.4 1.5
Flow Depth (ft)
Notes: USGS gage 11162620 rating data

Pilarcitos IWMP
Rating Curve for Pilarcitos Creek below Stone Dam
PWA Ref# 1884-T3A
P:\Projects\1884_Pilarcitos IWMP\Task3A_AssessmentUpdate\Figures\SD rating V2.doc

Streamflow Gain Below Stone Dam
180
25th Percentile
Median
160 75th Percentile
140
120
.
Discharge (cfs)
100
80
60
40
20
0
Date
Notes: from USGS gage data. Note period of record differs from period in Figure XX (Pilarcitos Hydrograph at HMB).
Pilarcitos IWMP
Streamflow Gain Between Stone Dam and Half Moon Bay
PWA Ref# 1884-T3A
P:\Projects\1884_Pilarcitos IWMP\Task3A_AssessmentUpdate\Figures\Pilarcitos Gain V2.doc

Proportion of Flow at Half Moon Bay from Lower Watershed
1.20
1.00 Delete this Paragraph and Insert Image Here
0.80
.
Proportion (%)
0.60
0.40
0.20
0.00
Oct Nov Dec Jan Feb Mar Apr May Jun Jul Aug Sep
Notes: lower watershed includes all contributing area below Stone Dam.
Pilarcitos IWMP
Proportion of Flow from Lower Watershed
PWA Ref# 1884-T3A
P:\Projects\1884_Pilarcitos IWMP\Task3A_AssessmentUpdate\Figures\lowerFlow V2.doc

100,000
Annual Flow (ac-ft)
10,000
1,000
100
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
Exceedance Probability
f i g u r e 20
Pilarcitos IWMP
Annual Flow Exceedance Pilarcitos at Half Moon Bay

PWA Ref# 1884
P:\Projects\1884_Pilarcitos IWMP\Task3A_AssessmentUpdate\Figures\\Mean_Annual_Q.xls
L
BP
SA
Tracy
WTP
CS
1
PL
PL
SA
3
SS
PL
Sa
Abandoned
vd
CS
Bl
n
st
PL
re e
3
An
Av
ll c
Hi e
dre
bra
l
as
Mi l
Re
CS
ser
PL
1&
CS
vo
Destroyed SS PL 2
l PL 3
ir
nn
e Dr
Tu a le
av
is El. 449' Trous d
El. 864'
D
Burlingame
Dr
a le
l sd
HIl
Sa
w
ye
Sa
r Ri
n
Ma
teo
CSP
Crocker Pipeline
Ck
L1
dg
CSP
L2
e
SS
PL
San Mateo Ck
Dam #1
(Mud Dam)
El. 646' l2
e
Hillsborough
nn
Tu
Pil a
1
rc it
l
ne
R es os
n
Tu
Go
e rvo Rd
el
ne
nn
lf
ir
HIL L
Tu
y
Co
Ha
El. 699'
ur
TUNN
d
C
R
se
tn
CS
M
ah
EL
-S
k
San Mateo Ck
c
Lo
Bla
A
Dam #2
Pi
il
pe
we
l El. 526'
li n
I-2
e
Rd
r
(F
R 80
or
gs
Cr
ce
id
in
M
Spr
an
ys
ai
S
Ma
n)
g
t al
Crystal
te oC
Pil
arc
e k
Sp
i o
ri n
t
sC
gs
k
Re
L
SP
ser
2, S
1&
PL
vo
CS
ir
l2
Legend
D
Crystal
nne
MG
Stone Dam Springs CS Pump Stn

Tu
Gauges El. 554'

40
Dam
Tunnel 1 El. 284'
existing, stream gauge
proposed, stream gauge USGS stream gauge

Valve S60
existing, reservoir stage gauge Half Moon Bay
1884Pilarcitos/Task3A-Assessment/Figs/WaterSupplyNetwork.ai
CC
Meters
WD
proposed, reservoir stage gauge

1
2"
proposed, flow meter
Water Conveyances
(with flow direction)
pipeline CCWD pipelines maintained by
Coastside County Water To
Half Moon Bay CCWD 18"
pipeline - pumped
tunnel
permanent stream
Hydrology - lines CCWD
2
y9
Permanent Stream Hw Pump
Station
Intermittent Stream
Flume (abandoned)
0 1 Miles
SFPUC Land Ownership
Natural Resources Division f i g u r e 21

Source: Hand drawn map by J. Chester 9/06
Elevations are USGS Mean Sea Level (NGVD 1929) datum
Basemap data from USGS DLG and SFPUC GIS Pilarcitos IWMP
J.Lukins 4/30/07 psv_gauges.mxd

Water Supply Network
PWA Ref# 1884-T3A
Source: San Francisco Public Utilities Commission
San Andreas Reservoir
# Water Diversions (1996)
! Water Diversions (2007)
Lower Crystal Springs Reservoir

Stone
# Dam
!!
!
Skyline Quarry
! !
!
! #
! Upper Crystal Springs Reservoir
Nu
Co rrin da Lo
ff C
#
ree
# ! ## Alb
e!
!!
k
!
!
rt C
s Tr
# #
any
Ap
an
!!no ! !# #
on
co
#
a
!
s
#
l io
C re
##
ek
!#Cr eek
k
#
ee
s
i to
Cr
rc
#! ! ! i!
la # #
M#
na
ad o n
P
!
#
##
C r eek
ls
!
il
M
!
!# !#
!
!!!#
n
!
o
Le
!A r!
r oy
o
Source: USGS (DRG), SFPUC (water bodies), 2007 Water

Diversions were downloaded from the WRIMS State Water figure 22
Resources Control Board database on June 21, 2007.
±
Pilarcitos IWMP
Water Diversions from 1996 to 2007
0 0.5 1 2
\\Sfo1\GIS\Pilarcitos\Pilarcitos_SWRCB_WtrDiversions.mxd
Fault
spfg
Geologic Units
Artificial Fill
Tss fl fs Colluvium
fc
fg fg Alluvial fan and Stream deposits
Sand Dune and Beach Deposits
Tss fl fl
Pilarcitos Reservoir Alluvium
flfs sp
Sedimentary Rock
KgrTss
Metamorphic Rock
Volcanic Rock
Tss fgfl fg
fs
l
nne
Tu
KJf c
s
i to
P ila r
Stone Dam Kgr fsfg
spfg fl flfg
Kgr KJf fs
fl
m
fg
fl Skyline Quarry
fl
Jgb
Nu
Corrin da Lo
Upper Crystal Springs Reservoir

ff
C
fsr
ree
Tm Tm Al
k
Tm
Tlo Kgr be Ka
Kgr rt C
s Tr
Tlo Tlo Tlo Tmb any

Tla
Ap
Tm
an
an
Tm ol Tp Ks
on
cos
io
C re
Tm Tm Tmb
ek
Tp ek
Cr e
k
Tmb
ee
Qmt os Tm
it
Cr
rc
ila
na
M ad o n
P
TmbTmb
Tvq Tw
Qmt
ee k Tla
Qmt Cr
ls
il
M
Qmt Tp
Qmt Tmb
Tp
n
o
Le
o
Ar r o y
Source: USGS (DRG, DEM, Geology), SFPUC (water bodies)

figure 23
±
Pilarcitos IWMP
Geologic Units and Surface Deposits
0 0.5 1 2
\\Sfo1\GIS\Pilarcitos\Pilarcitos_Geology.mxd
e l
nn
Tu
s
lar
Pi
Stone Dam
Percent Sand in Soils (% Silt) Skyline Quarry

22 (28)
25 (53)
34 (37)
35 (34) Upper Crystal Springs Reservoir
Nu
Corrin da Lo
39 (37) ff C
re e
40 (38)
A lb
k
42 (37) e
rt C
s Tr
42 (38)
an y
Ap
an
43 (39)
no on
co
a
44 (40)
s
l io
63 (19)
Cree
65 (19)
k
ee k
Cr
k
65 (20)
ee
s
ito
Cr
66 (19) rc
ila
na
66 (15) M ad o n
P
67 (19)
67 (20)
68 (19)
C reek
68 (19) ls
il
M
68 (14)
82 (11)
96 (2)
Note: Values which do not

add to 100 percent represent n
o
Le
soil units which contain a o

A rr o y
certain percentage of clay.
Gray areas indicate Missing Data.
Source: USGS (DRG, DEM), SFPUC (water bodies), NRCS (soils)

figure 24
±
Pilarcitos IWMP
Soil Particle Size
0 0.5 1 2
\\Sfo1\GIS\Pilarcitos\Pilarcitos_SoilSand.mxd
Hillslope Failure and Channel Erosion
# # 1982 Debris Flows
# # # # # Bank Erosion (PWA, 96)

# #
## #
###
### ## # # # Gully (PWA, 96)
### ### #
#
#
##
# #
##
# Landslide (PWA, 96)
# #
##
## ## $ Road related (PWA, 96)
## ## #
# # #
# # Pilarcitos Reservoir
#
# ###
#
Upper Pilarcitos
# #
# # #
# #
# Lower Crystal Springs Reservoir
#
Stone
#
# Dam
##
#
#
###
# ###
# #
###
# ### # #
## #
# ## #
Apanolio
Skyline Quarry
# ###
# ## ## ## #
#### # # # # #
## # ##
# # ## ## #
# #
## #
## # # Nuff Creek#
# ## # ##
Corrinda #
# Los #Trancos
# Upper Crystal Springs Reservoir
##
#####
#
#
# # # #
### ## ## ## #
# # # $
# # # ## # Albert#Canyon
# #
### # # #
Middle Pilarcitos
# ###
# # #
# # # ##
# ##
# # # ##
## # # #
# # #
#
#
$ # #
# ## #
Madonna Creek ##
Lower Pilarcitos #
# # ## #
#
# # # # ### ## #
# # ##
#
# # #
# # # Creek ## #
# # #Mills # ### # ##
# ## ## #
# ##
### # ## # # # #
# #
Lower Arroyo Leon# # # # #
# # ###### # # #
### #
# ## # #
# ### #### #
#
###### # # # ####
#
### #
##
## #
# # ## # # #
# ## # ##
# # ##
## $ # #Upper # #
Arroyo Leon
# # #
## ##### #
# # ###
##
#### #
$ #
# #
$####
### ####
#
## #
#
Source: USGS (DRG, Debris Flows), SFPUC (water bodies),

PWA (Bank Erosion, Road Related Erosion, Landslides, Gullies) figure 25
±
Pilarcitos IWMP
Hillslope Failure and Channel Erosion
0 0.5 1 2
\\Sfo1\GIS\Pilarcitos\Pilarcitos_SlopeHazard_USGS.mxd
Channel Length Greater Than 60% Slope
Regulated Reach
Stone Dam Reach
Nuff
Cordina Los Trancos
Apanolio
Madonna
Middle Pilarcitos
Lower Pilarcitos
Lower Arroyo Leon
Mills
Upper Arroyo Leon
0% 2% 4% 6% 8% 10% 12% 14% 16% 18%

Proportion of Total Channel Length
Notes: f i g u r e 26
Channel Grade Summary

PWA Ref#1884-T3A
P:\Projects\1884_Pilarcitos IWMP\Task3A_AssessmentUpdate\Figures\\ChGrad Summary.xls

Slope Hazard Classifications
No Risk (0- 30%)
Minimal Risk (30- 45%)
Modest Risk (45- 60%)
High Risk (60- 75%)

Very High Risk (75- 90%)
Pilarcitos Reservoir Highest Risk (>90%)

Stone Dam
Skyline Quarry

Nu
Corrin d a Lo
ff C
re e
A lb
k
rt C
T ra s
any
Ap
nc
no on
a
os
l io
C ree
k
ee k
Cr
k
ee
s
ito
Cr
rc
ila
na
M ad o n
P
C r eek
ls
il
M
n
o
Le
o
A rr oy
Source: USGS (quadrangle, dem), SFPUC (water bodies)

figure 27
±
SWC (Slope classifications)
Pilarcitos IWMP
Watershed Slope
0 0.5 1 2
\\Sfo1\GIS\Pilarcitos\Slope Hazard.mxd
Road Classification (SFPUC)
trail
unpaved road
paved road; secondary highway
primary highway
ramp

Stone Dam
Skyline Quarry

Nu
Corrin da Lo
ff C
re e
A lb
k
rt C
s Tr
an y
Ap
an
no on
co
a
s
l io
Cree
k
ee k
Cr
k
ee
s
ito
Cr
rc
ila
na
M ad o n
P
C reek
ls
il
M
n
o
Le
o
A rr o y
Source: USGS (DRG, DEM), SFPUC (roads, water bodies)

figure 28
±
Pilarcitos IWMP
Partial Road Map
0 0.5 1 2
\\Sfo1\GIS\Pilarcitos\Pilarcitos_Roads.mxd
Stream Gradient
Pool-Riffle (0 to 2.5%)
Plane Bed (2.5 to 4%)
Step-Pool (4 to 8%)
Cascade (8 to 15%)
Headwater Drainage (>15%)
el
nn
Tu
s
to
i
Pilar c
Stone Dam
Skyline Quarry
N uf
C or rind a L

fC
r
ee
k
Al
be
os
rt
Ap
C
Tra
a ny
an
li
nc
o
on
o
os
C re
ek
e k
e ek
Cre
s
to
Cr
r ci
na
a Ma
do n
Pi l
k
r ee
sC
ill
M
n
o
Le
o
Ar r o y

figure 29
±
Pilarcitos IWMP
Stream Gradient in the Pilarcitos Watershed
0 0.5 1 2
\\Sfo1\GIS\Pilarcitos\StreamGrad.mxd
Exceedence 95% Confidence Interval Weibull
5,000
4,500
4,000
3,500
Peak Discharge (cfs)

3,000
2,500
2,000
1,500
1,000
500
0
1 0.1 0.01
Exceedence Probability
(log scale)
Notes: USGS Station xxx (Pilarcitos Creek at Half Moon Bay) f i g u r e 30

Annual Peak Discharge Probability Pilarcitos Creek at HMB

PWA Ref# 1884
P:\Projects\1884_Pilarcitos IWMP\SWC Analysis\Hydrology\peak flows.xlsHorzFigureBox

San Andreas Lake
ale Ca
Trousd ul
a
lifo
Sa Cr e Legend ns r ni 101
ek
n P ed a st o n e ni a
ro Cre
k
P Sa
De
Cree
ek
da
dale n
la
E
Oak
n
Pilarcitos Creek Watershed M
wa
bu
at
re
eo
c h ez
Occ
o n lo r i
n
Hillsb
82
CWHR Vegetation r lto
Ti
ls t F
id
a
t
pl
mi
San
San Pedro
Pedro Valley
Valley County
County Park
S an
e n ta
Park
o ro u
Annual Grassland Po
m
to h
erri d 4t
Su
Ra
i tos C El C 3r
l
Mcnee
Mcnee Ranch
Ranch State
State Park
Park a rc ez
gh
re
Pil e Closed-Cone a
In
Pine-Cypress h
nt 5t
o
Sa
au
h
un d
9t
S an
te
k
gs
Cropland
ha
aym
rin
C
Ma
Sp
Ed
o
nR
Coastal Scrub
i
l
nb
Cr
ta
te
ys
ur
Sa
ek
Cr
gh
e
Pilarcitos Lake Douglas-Fir
yn
e
Ha
Lacustrine
Pila
in
Lower Crystal Black Mounta
r eek
rc i
Springs Reservoir Mixed Chaparral
e Cr
nt
to s
C
ee
ice k 280
V Montane Hardwood
an e
re 280
k
nC Redwood
th
ree
S
el
t o C Laur
28
teo
is Pa
nn Ma Urban
rro
tt ee
Cr
De n Po k
Sa l
L oc k
he
za
m
An
sC
us
De
Po
ek
Cr
re
lhe
ee
mu
k
s
Ralsto
ree
92 n
rC
Half Moon Bay 92

r r oyo
ee
D
eek
io, A
San Mateo
l i o Cr
Can
ada
M ed
Corin
o
an
1
En
Ap
92
da L os T r
e
Upper Crystal
D
Springs Reservoir
Cre e
a nc
ns
a
hm
os
r e nc
F
Cr e
ek
35
ek
on
Le
,A
e
Cr
r ro Ma n
yo do n
a
1
Kelly
1st
Main
Central
reek
Filbert sC
i ll
1st
Ar
M
ro y o Le Burleigh
Burleigh Murray
Murray Ranch
Ranch St
St Park
Park
Half
on
Moon 1
Bay
Purisima
1 Cr e
ek
figure 31
Pilarcitos IWMP
California Wildlife Habitat Relationship (CWHR) Vegetation Data
Feet HTH Ref. # 2772-01
0 3,250 6,500 13,000
MATCH
MATCHLINE
LINE
Legend
Willow - Alder Riparian Forest
Willow Mixed Riparian Forest
Willow Riparian Forest
Eucalyptus - Alder Riparian Forest
Eucalyptus Grove
Source: The Habitat Restoration Group in PWA 1996
figure 32
Pilarcitos IWMP
Locations of Riparian Plant Communities and Eucalyptus Groves
Feet
0 1,000 2,000 4,000 HTH Ref. # 2772-01
Legend
Willow - Alder Riparian Forest
Willow Mixed Riparian Forest
Willow Riparian Forest
Eucalyptus - Alder Riparian Forest
Eucalyptus Grove
MATCHL
MATCHLINE
INE
figure 33
Pilarcitos IWMP
Locations of Riparian Plant Communities and Eucalyptus Groves
Feet
0 1,000 2,000 4,000 HTH Ref. # 2772-01
MATCH
MATCHLINE
LINE
Legend
German Ivy
Bristly Ox Tongue
Non-native Conifer (Pine, Cypress)
Eucalyptus
French Broom
Nasturtium
Periwinkle
Pampas Grass
Poison Hemlock
Thistle Species
figure 34
Pilarcitos IWMP
Locations of Significant Concentraions of Invasive, Non-native Plant Species
Feet
0 1,000 2,000 4,000 HTH Ref. # 2772-01
Legend
German Ivy
Bristly Ox Tongue
Non-native Conifer (Pine, Cypress)
Eucalyptus
French Broom
Nasturtium
Periwinkle
Pampas Grass
Poison Hemlock
Tradescantia
Thistle Species
MATCHL
MATCHLINE
INE
figure 35
Pilarcitos IWMP
Locations of Significant Concentraions of Invasive, Non-native Plant Species
Feet
0 1,000 2,000 4,000 HTH Ref. # 2772-01
Lind San Andreas Lake
Seb
e
in
aM
el
ar
on
Ad
asti
ide
ale
Trousd
t
Eas
lls
Al
a
82
va
Hi
ra
do ta
eli Sh
aro
r m n
Ca Eu
ta ca
lyp
Vis tus
lla
San
San Pedro
Pedro Valley
Valley County
County Park
Park Be
on
st
al
it
m
R
m
Su
au
a te
Ch
280
Pilarcitos Lake
280 e
yn
Ha
h
35 ug
o ro
se
rl b
ni
a
De
M
Legend Lower Crystal Springs Reservoir

San Mateo
Pilarcitos Creek Watershed
Vegetation Communities
Douglas Fir / Redwood Forest
Douglas Fir / Redwood Forest - (Old Growth)
Exotic Forest - Monterey Cypress
Mixed Evergreen Forest / Coast Live Oak Woodland
Riparian Forest - Arroyo Willow
Riparian Forest - White Alder
Northern Coastal Scrub
Av enue Cabrillo
Northern Coastal Scrub w/ Trees
Chaparral - Mixed
Chaparral - Northern Maritime
1
Grassland - Non-native 92
Grassland - Serpentine Bunchgrass

35
Pond or Reservoir
Urban or Bare
Data compiled by ESA, Inc. and Diane Renshaw (1993-94)
Provided by EDAW, Inc. - San Francisco
Ma
in
figure 36
Pilarcitos IWMP
Vegetation Communities
0 2,500 5,000 10,000
Golden
Golden Gate
Gate National
National Rec
Rec Area
Area
San
San Francisco
Francisco collinsia
collinsia Choris'
Choris' popcorn-flower
popcorn-flowerwhite-rayed
white-rayed pentachaeta
pentachaeta
Franciscan
Franciscan thistle
thistle Choris' popcorn-flower
Choris' popcorn-flower SanSan Francisco
Francisco owl's-clover
owl's-clover
coast
coast yellow
yellow leptosiphon
Millbrae
leptosiphon San
San Francisco
Francisco collinsia
collinsia
Franciscan
Franciscan onion
onion
Pacifica 35
San
San Pedro
Pedro Valley
Valley County
County Park
Park
Burlingame
Montara
Montara manzanita
manzanita Montara
Montara manzanita
manzanita Valley
Valley Needlegrass
Needlegrass Grassland
GrasslandSerpentine
Serpentine Bunchgrass
Bunchgrass
Northern
Northern Maritime
Maritime Chaparral
Chaparral Crystal
Franciscan
Franciscan thistle
thistleMontara Crystal Springs
Springs lessingia
lessingia Northern
Northern Coastal
Coastal Salt
Salt Marsh
Marsh
Montara manzanita
manzanita Indian western
western leatherwood
leatherwood
Indian Valley
Valley bush
bush mallow
mallow Hillsborough
Northern
Northern Maritime
Maritime Chaparral
Chaparral Hillsborough chocolate
chocolate lily
lily
Mcnee
Mcnee Ranch
Ranch State
State Park
Park Hall's
Hall's bush
bush mallow
mallow
Montara
Montara manzanita
manzanita fragrant
fragrant fritillary
fritillary
Franciscan
Franciscan onion
onion Franciscan
San
San Francisco
Francisco gumplant
gumplantKings
Kings Mountain
Mountain manzanita
manzanita Franciscan onion
onion
Davidson's
Davidson's bush
bush mallow
mallow
Valley
Valley Needlegrass
Grassland
Hickman's
Hickman's cinquefoil
cinquefoil San
San Francisco
Francisco collinsia
collinsia
Hickman's
cinquefoil fragrant
fragrant fritillary
fritillaryValley
Valley Needlegrass
Grassland
Montara
Montara manzanita
manzanita
1 Northern
Northern Coastal
Coastal Salt
Salt Marsh
Marsh
Hillsborough
Northern
Northern Maritime
Maritime Chaparral
Chaparral San
San Mateo
Mateo woolly
woolly sunflower
sunflower Marin
Marin western
western flax
flaxSan
San Mateo
Mateo woolly
woolly sunflower
sunflower
Northern
Northern Maritime
Maritime Chaparral
Chaparral Marin
Marin western
western flax
flaxSan
San Francisco
Francisco collinsia
Foster City
collinsia
Hickman's cinquefoil Point
Point Reyes
Reyes bird's-beak
bird's-beak
western leatherwood Crystal
Crystal Springs
Springs lessingia
lessingiaarcuate
arcuate bush
bush mallow
San Mateo
San
San Francisco campion western leatherwood
Francisco campion mallow
rose
rose leptosiphon saline
saline clover
clover
Montara
leptosiphon Serpentine
BunchgrassSan San Mateo
Mateo woolly
woolly sunflower
sunflower
Marin
Marin western
western flax
flaxSan
San Mateo
Mateo woolly
woolly sunflower
sunflower
Hickman's
cinquefoil bent-flowered
bent-flowered fiddleneck
fiddleneck
rose
rose leptosiphon
leptosiphon Crystal
Crystal Springs
Springs lessingia
lessingia
San
San Francisco
Francisco collinsia
collinsia
Moss Beach Marin
Marin western
western flax
flax
Half Moon Bay Serpentine
Bunchgrass Davidson's
Davidson's bush
bush mallow
mallow Northern
Northern Coastal
Coastal Salt
Salt Marsh
Marsh
Crystal
Marin
Marin western
western flaxflax Highlands-Baywood Park
Crystal Springs
Springs lessingia
lessingiafragrant
fragrant fritillary
fritillary Hall's 101 Point
Point Reyes
Reyes bird's-beak
bird's-beak
Hall's bush
bush mallow
mallow
Crystal
Crystal Springs
Springs lessingia
lessingia
Northern
Northern Coastal
Coastal Salt
Salt Marsh
Marsh San
San Francisco
Francisco Bay
Bay spineflower
spineflower Belmont
coastal
coastal marsh
marsh milk-vetch
El Granada
milk-vetch San
San Mateo
Mateo thorn-mint
thorn-mint
western
western leatherwood
leatherwood
San Mateo Franciscan
Franciscan onion
onion
coastal
coastal marsh
marsh milk-vetch
milk-vetch
Legend
Kellogg's
Kellogg's horkelia
horkelia arcuate
arcuate bush
bush mallow
mallow 82
San Carlos
Sensitive Terrestrial Communities 92 Redwood City
General Area western

western leatherwood
leatherwood
arcuate
arcuate bush
bush mallow
mallow
Choris'
popcorn-flower San
San Mateo
Mateo thorn-mint
thorn-mint
Special-status Plant Species Crystal
Crystal Springs
Springs lessingia
Serpentine
lessingia
Bunchgrass North Fair Oaks
Half Moon Bay white-rayed
white-rayed pentachaeta
Specific Location
pentachaetaSan
San Mateo
Mateo thorn-mint
thorn-mint
35 western
western leatherwood
leatherwood
Emerald Lake Hills

Choris'
popcorn-flower Burleigh
Burleigh Murray
Murray Ranch
Ranch St
St Park
Park
Santa
Santa Cruz
Cruz manzanita
manzanita fragrant
fragrant fritillary
fritillary
Choris'
popcorn-flower 280
Approximate Location
Kings
Kings Mountain
Mountain manzanita
manzanita San
San Mateo
Mateo thorn-mint
thorn-mint
Choris'
popcorn-flower
Marin
Marin western
western flax 84
2-
Atherton
flax
m
ile
General Area
Huddart
Huddart County
County Park
Park
ra
Kings
Kings Mountain
Mountain manzanita
manzanita Kings
Kings Mountain
Mountain manzanita
manzanita
Menlo Park
di
Kings
Kings Mountain
Mountain manzanita
manzanita Franciscan
Franciscan onion
onion
us
Santa
Santa Cruz
Cruz manzanita
manzanitaKings
Kings Mountain
Kings
Mountain manzanita
Kings Mountain
manzanita
Mountain manzanita
manzanita
Woodside San
San Francisco
Francisco collinsia
collinsia
Pilarcitos Creek Watershed arcuate

arcuate bush
bush mallow
mallow
West Menlo Park
western
western leatherwood
leatherwood
Kings
Kings Mountain
Mountain manzanita
manzanita Franciscan
Franciscan onion
onion
Kings
Kings Mountain
Mountain manzanita
manzanita fragrant
fragrant fritillary
fritillarySerpentine
Bunchgrass
Wunderlich
Wunderlich County
County Park
Park
figure 37
Pilarcitos IWMP
California Natural Diversity Database (CNDDB) Plant Records
Feet
0 4,000 8,000 16,000 HTH Ref. # 2772-01
big California
California red-legged
red-legged frog
frog
big free
free -tailed
-tailed bat
bat
Golden
Golden Gate
Gate National
National Rec
Rec Area
Area
California
red-legged frog
frog pallid
pallid bat
bat
California
California clapper
clapper rail
rail
double-crested
double-crested cormorant
cormorant
monarch
monarch butterfly
butterfly
Steelhead
Steelhead -- Central
Central California
California Coast
Coast ESUs
ESUs
Millbrae San
San Francisco
Francisco Forktail
Forktail Damselfly
Damselfly
California
California clapper
clapper rail
rail
Pacifica Mission
Mission blue
blue butterfly
butterfly
California
red-legged frog
frog Burlingame
San
San Pedro
Pedro Valley
Valley County
County Park
Park 35 California
California clapper
clapper rail
rail
California
red-legged frog
frog
San
San Bruno
Bruno elfin butterfly San
elfin butterfly San Bruno
Bruno elfin
elfin butterfly
butterfly
San
San Francisco
Francisco lacewing
lacewing
American
American badger
badger
Mcnee
Mcnee Ranch
Ranch State
State Park
Park California
red-legged frog
frog Myrtle's
Myrtle's silverspot
silverspot
Alameda
Alameda song
song sparrow
sparrow
California
red-legged frog
frog Ricksecker's
Ricksecker's water
water scavenger
scavenger beetle
beetle
California
California clapper
clapper rail
rail
California
red-legged frog
frog California
California black
black rail
rail
1
Hillsborough Foster City
Montara San Mateo western
western snowy
snowy plover
plover
Edgewood
Edgewood blind
blind harvestman
harvestman
salt-marsh
salt-marsh wandering shrewwhite-tailed
wandering shrew white-tailed kite
kite
salt-marsh
salt-marsh harvest
harvest mouse
mouse Alameda
Alameda song
song sparrow
sparrow
California
red-legged frog
frog northern
northern harrier
harrier
California
red-legged frog
frog short-eared
short-eared owl
owl
Moss Beach
California
Half Moonred-legged
Bay frog
frog Bay
Bay checkerspot
checkerspot butterfly
butterfly
California
California least
western
western snowy
least tern
tern
snowy plover
plover
pallid
pallid bat
bat
salt-marsh
salt-marsh harvest
harvest mouse
Legend
Alameda
Alameda song
song sparrow
sparrow mouse
California
El Granada
red-legged frog
frog
Steelhead
Central California
California Coast
Coast ESUs
ESUs Highlands-Baywood Park California
California clapper
clapper rail
rail
Bay
Bay checkerspot
butterfly salt-marsh
salt-marsh harvest
harvest mouse
mouse
saltmarsh
saltmarsh common
common yellowthroat
yellowthroat
Special-status Animal Species
California
red-legged frog
frog
California
red-legged frog
frog
Belmont Alameda
Alameda song
song sparrow
sparrowwestern
western snowy
snowy plover
plover
California
California clapper
clapper rail
rail
Specific Location San Mateo
California
red-legged frog
frog
saltmarsh
saltmarsh common
common yellowthroat
yellowthroat
Alameda
Alameda song
song sparrow
sparrow
Alameda
Alameda song
song sparrow
sparrow
California
red-legged frog
frog California
California least
least tern
tern
Steelhead
Central California
California Coast
Coast ESUs
ESUs
Approximate Location saltmarsh

saltmarsh common
common yellowthroat
yellowthroat
saltmarsh
saltmarsh common
common yellowthroat
Ricksecker's
yellowthroat
Ricksecker's water
water scavenger
scavenger beetle
beetle
San Carlos 82 101
monarch
monarch butterfly
butterfly 92 saltmarsh
saltmarsh common
common yellowthroat
yellowthroat
Santa
Santa Cruz
Cruz kangaroo
kangaroo rat
rat
General Area
saltmarsh
saltmarsh common
common yellowthroat
yellowthroat
California
red-legged frog
frog
Bay
Bay checkerspot
butterfly
Edgewood
Edgewood blind
blind harvestman
harvestman Redwood City
San Francisco Garter Snake Edgewood
Edgewood Park
Park micro-blind
micro-blind harvestman
harvestman
Anecdotal Location Half Moon Bay Bay

Bay checkerspot
butterfly
California
red-legged frog
frog
Burleigh
Burleigh Murray
Murray Ranch
Ranch St
St Park
Park Emerald Lake Hills
California Red-legged Frog 35 280
Bay
Bay checkerspot
butterfly American
American badger
badger
Anecdotal Locations 84
Atherton
Existing Potential Amphibian /
2-
m
Reptile Breeding Ponds

ile
Huddart
Huddart County
County Park
Park
California
California tiger
tiger salamander
salamander
ra
(based on aerial imagery from 2005) Menlo Park

di
pallid
pallid bat
bat California
red-legged frog
frog
us
CaliforniaWest
California
Menlo
red-legged
red-legged frog Park pallid
frog pallid bat
bat
California California red-legged frog
California red-legged frog
red-legged frog
frog
western
western pond
pond turtle
turtle
Woodside American
American badger
badger
Santa
Santa Cruz
Cruz kangaroo
kangaroo rat
rat
Wunderlich
Wunderlich County
County Park
Park
figure 38
Pilarcitos IWMP
California Natural Diversity Database (CNDDB) Animal Records
Feet
0 4,000 8,000 16,000 HTH Ref. # 2772-01
Legend
Marbled Murrelet Critical Habitat
Approximate Location of 2005/2006 Detections

(Source: Avocet Research Associates 2006)
Area Containing Potential Nesting Habitat

(Source: Avocet Research Associates 2006)
figure 39
Pilarcitos IWMP
Marbled Murrelet Habitat / Occurrences
0 2,000 4,000 8,000
Appendix A
Geospatial Map Inventory
Geospatial Map Inventory

Spatial Data Acquistion Table for Pilarcitos Watershed
Category GIS Data Layer Data Source Description

Aerial Imagery B & W DOQQ (Seamless) USGS
Color Orthoimagery USDA NAIP
USGS Seamless Topo Quad USGS/USDA/NRCS
Historic USGS quads BARD/USGS
96 Rest. Plan Constraints PWA '96
96 Rest. Plan Erosion PWA '96
96 Rest. Plan Wtr Diversions PWA '96
Raster Data USGS Digital Elevation Model (DEM) USGS
Feature Data Watershed Boundary PWA/USGS
Subbasin Boundaries PWA/USGS
Drainage Lines PWA/USGS
Groundwater Basins USGS/CaSil
Soil Map Units NRCS/USDA
Mean Annual Precipitation PRISM/NRCS
Bank Erosion Sites PWA '96
Gully Locations PWA '96
Road related erosion PWA '96
Landslides PWA '96
Water Diversions PWA '96
Fish Passage Barriers Pacific State Marine Fisheries Commission
Upstream Steelhead Migration PWA '96
Downstream Steelhead Migration PWA '96
Contours SFPUC Contours - USGS (25ft and 40ft contour interval depending on quad)
PLSections SFPUC Public Land Survey (Sections) - USGS
PowerLines SFPUC Power and transmission lines - USGS
Railroads SFPUC Railroads - USGS
Roads SFPUC Roads - USGS, updated by LRMS
SfpucOwn SFPUC SFPUC land ownership
UTMGrid SFPUC SFPUC alpha-numeric grid based on UTM NAD27 grid
Aquahab_ln SFPUC Aquatic Habitat - lines
Aquahab_py SFPUC Aquatic Habitat - polygons (reservoirs)
Easements SFPUC Scenic and Recreation easements
EcoSensi SFPUC Ecological Sensitivity
ErosionSensi SFPUC Erosion Vulnerability Composite
FireDefense SFPUC Fire Defense points - tanks, hydrants, heliports. Existing and proposed.
FirePlan SFPUC Fire Management Plan - proposed treatments for fuel reduction
FireSev SFPUC Wildfire severity composite vulnerability
Gates SFPUC Gates
Rainfall SFPUC Rainfall Intensity Zones
RoadCodes SFPUC Summary Table of LRMS and Maximo codes for watershed roads. Attributes also stored in ROADS layer
SlideSusc SFPUC Landslide Hazards
SSAnimalsPotential SFPUC Potential habitat for Special Status animals
SSAnimals_pt SFPUC Special Status Animals (Reported) Points
SSAnimals_py SFPUC Special Status Animals (Reported) polygons
SSHabitat SFPUC Table of Special Status species habitats - joins to Vegetation layer
SSPlants SFPUC Special Status Plants - polygons
SSStatusCodes SFPUC Special Status Species code descriptions
SSVegComm SFPUC Special Status Vegetation Communities
Trails_ln SFPUC Trails - lines
Trails_pt SFPUC Trails - points
VegCover SFPUC Vegetation Canopy Cover with % cover class
Vegetation SFPUC Vegetation Communities (mapped by Jones & Stokes for HCP Oct 2003)
VegMonitor SFPUC Vegetation monitoring sites
WMP_StudyArea SFPUC Study area boundary for 2001 Watershed Management Plan
WQVuln SFPUC Composite of Water Quality Vulnerability
P:\Projects\1884_Pilarcitos IWMP\Task3A_AssessmentUpdate\Appendices\AppendixB_Spatial_Data_Library.xlsDataAcquisition_Source
Appendix B
Oral Histories Pertaining to IWMP
Oral Histories Pertaining to IWMP

ORAL HISTORY REPORT
We are collecting Oral Histories from local stakeholders as part of the ongoing development of
the IWMP to explore additional information resources that may be available for the watershed. A
specific set of questions was asked of each stakeholder, and we attempted to summarize their
response. It may be necessary to clarify certain responses by contacting these stakeholders again,
and in some cases, we were unable to contact certain stakeholders. This Appendix includes the
responses collected to date.
Jim Salerno
SFPUC
¾ We have a number of technical reports and studies that have been made available to us.
Are you aware of any data or information not available in existing reports? (i.e. photos,
maps, observations, etc.);
o A draft report documenting field survey work for last autumn is in production,
and will provide fish information, etc. SFPUC will make this report available as
soon as it has completed its internal review.
¾ Can you describe any significant effects of large storms (’55, ’64, ’82)?
o No additional information to share as he wasn’t present at the time.
¾ Can you offer sense of any significant changes in land-use practices that might have
affected the watershed?
o Talk with Joe Naras or Joanne Wilson (in Watershed Land Management Group)
¾ Do you have any specific issues or concerns that the workgroup should consider in its
planning process?
o SFPUC issues have been discussed within the IWMP process, and SFPUC will
continue to engage in the process to ensure that their positions ar reflected in the
plan.
P:\Projects\1884_Pilarcitos_IWMP\Task4_IWMP\reports\1884-
00_Wshed_Assess_Update\Appendicies\1884_AppendixB_Oral_Histories_122807V2.doc 1
JoAnne Wilson
SFPUC
o Not much beyond what is on the website. Can help with more specific requests
if needed.
o Refer to Joe Naras.
o The most signficant changes in land-use practices stem from the Commission's
adoption of the Peninsula Watershed Management Plan which includes best
management practices ("management actions") and policies. Chapter 6 of the
Watershed Management Plan describes the status of these management actions.
The SFPUC has also initiated the process to develop a Habitat Conservation Plan
(HCP) for the Peninsula Watershed, which could also change the way we manage
the land.
planning process?
o I hope that the IWMP for the Pilarcitos Watershed will include the SFPUC's
policies and management actions from the Peninsula Watershed Management
Plan.
Hank Sciaroni
Nurseryman on mainstem Pilarcitos Creek
o RCD should have all materials, as they’ve been provided to them for some time.
o Creek busted [eroded] its banks when water was released (Chris Fischer at RCD
knows about this). Tim Frahm has record. Bank materials for reconstruction
were obtained from road widening (Hwy 92 project).
o Water releases always damage their properties
o Held emergency meetings with Ed Fonseca at the time. Office of emergency

services was supposed to handle communications during major events, but has
yet failed to do so.
o Little hay grown on hills these days.
o Coselino & Nurseryman no longer active
o Retained water rights & riparian. Passed them onto the RCD.
o Recycled water for Nurserymans Exchange
o Only pumped when sufficient water was available
o Less farming on the stream then historically
o No pumping during dry years. Pumping greatly reduced in recent years.
planning process?
o No
o Stream should be in better shape today than ever.
o We’d all be better off if SFPUC kept water in Pilarcitos and stopped diverting to
the “other side”
o Need to consider unplugging overflow pathway for the Pilarcitos dam site
Gil Gossett
Nurseryman on Aponolio Creek
o Video tape by fish & game (upstream) – by CF&G (Sacramento)
o Video (Lenny Roberts) from headwaters
o 1982 washed out everything. Government road to antennas (Air Force) used to
dump a lot of water into the canyon. 3-4 feet of sand. Apanolio Creek. In
august, culvert will be replaced with bridge (RCD project).
o Lots of erosion. Less silt in recent years. Lots when BFI was considering
landfill (1980s). Used dam as silt trap, cleaned out every 2-3 weeks. Cut road
across canyon that generated lots of silt. Check with Keith Mangold.
planning process?
o Nothing specific. In 1974, lots of fish. Few in recent years.
o Two years ago, electroshocking – only 1 24” steelhead. CA F&G?
o Back in 1980s, boy caught 2 steelhead (20-30”) from pond for irrigation water.
¾ Other Thoughts
o Streamflow from Apanolio major contributors to Pilarcitos. 1946-48 city of

HMB got water from Apanolio. Concrete basin built in 1800s (Bongard’s
property).
o Steelhead run used to be very significant. Family used to catch steelhead.
o Has boxes of records from BFI. RCD had them for a while. Also has roll of
plans for BFI.
Stan Pastorino
Nurseryman on Mainstem Pilarcitos Creek (Between Apanolio and Corinda Los Trancos)
o No
o Had to elevate water tanks. Pilarcitos was 200-300 feet across. Dam release
from one of the dams
o Jim Coselino lost 2-3 crops of Xmas trees
o No
o Has 2-3 acres of greenhouses built in 1959 to as recent as 25 yrs ago. No recent
changes.
o POST owns parcels south of creek – no longer being farmed.
planning process?
o No
Appendix B
WORKGROUP MEMORANDUM OF UNDERSTANDING
Workgroup Memorandum of Understanding
Appendices
January 25, 2007
Memorandum of Understanding (MOU)
Among
California Department of Fish and Game, California State Parks, City of Half Moon Bay,
Coastside County Water District, Committee for Green Foothills, Gulf of the Farallones
National Marine Sanctuary, Half Moon Bay Fishermen’s Association, Midpeninsula
Regional Open Space District, Monterey Bay National Marine Sanctuary, National
Marine Fisheries Service, Peninsula Open Space Trust, Pilarcitos Creek Advisory
Committee, San Francisco Public Utilities Commission, San Francisco Bay Regional
Water Quality Control Board, San Mateo County, San Mateo County Farm Bureau, San
Mateo County Resource Conservation District, Sewer Authority Mid-Coastside, Surfrider
Foundation - San Mateo Chapter
Regarding
The Establishment of the Pilarcitos Creek Restoration Workgroup and the Development
of an Integrated Watershed Management Plan
I. Recitals
A. The groups listed above have been working together for many years under the
umbrella of the Pilarcitos Creek Watershed Restoration Project (Project). The
Project was created and funded by the California Department of Fish and Game
and the San Francisco Regional Water Quality Control Board as part of a
settlement between the State of California, Browning-Ferris Industries, and Apex
Oil Company for two separate pollution discharge events that occurred in 1992.
B. The Pilarcitos Creek Advisory Committee (PCAC) was formed to provide

local stakeholder input on the development of the Pilarcitos Creek Restoration
Plan (1996 Plan), and to provide advice and guidance to the Project Manager, the
San Mateo County Resource Conservation District (RCD). The 1996 Plan
identified five major issues of concern in the creek: 1) reduced streamflows, 2)
degraded fish habitat, 3) bank erosion and loss of riparian vegetation and habitat,
4) watershed erosion and channel sedimentation, and 5) exotic vegetation.
C. The groups listed above have decided collectively to convene the new
Pilarcitos Creek Restoration Workgroup (Workgroup) to develop an Integrated
Watershed Management Plan (IWMP) that would update the 1996 Plan and
address high priority issues in the watershed (e.g., Central Coast steelhead
protection and restoration). The PCAC will be a member of the new Workgroup.
II. Purpose of the Workgroup

The purpose of the Workgroup is to work as partners to balance all of the beneficial uses
of available water resources in the Pilarcitos Creek watershed and to find solutions that
protect the environment, agriculture, public health, domestic water supply, and economic
interests.
1
III. Purposes of this MOU
The purposes of this MOU are to:
A. Describe how the Workgroup operates as a collaborative forum to achieve the
common goal of protecting and restoring the natural resources of the Pilarcitos
Creek watershed.
B. Outline the process for developing the Pilarcitos Creek Integrated Watershed
Management Plan.
IV. Definitions The abbreviations and capitalized words and phrases used in this MOU
have the following meanings:
A. “CCWD” refers to Coastside County Water District.
B. “CDFG” refers to California Department of Fish and Game.
C. “HMB” refers to City of Half Moon Bay.
D. “IWMP” refers to Integrated Watershed Management Plan.
E. “NMFS” refers to National Marine Fisheries Service.
F. “RCD” refers to San Mateo County Resource Conservation District.
G. “SAM” refers to Sewer Authority Mid-Coastside.
H. “SFPUC” refers to San Francisco Public Utilities Commission.
I. “Party” or “Parties” refers to the organization(s) signing this MOU.
J. “Signatory” or “Signatories” refers to the person or group of people signing
this MOU on behalf of their organization(s). The Signatories are the General
Managers, Directors, Executive Officers, etc. from each organization, or their
designees.
K. “Workgroup” refers to the Pilarcitos Creek Restoration Workgroup.
L. “Workgroup Members” refers to the senior staff delegated by the Signatories
to represent their organization on the Workgroup.
V. Workgroup Principles, Organization, and Participant Roles

A. Convener of Workgroup Meetings: The RCD will serve as the convener of
Workgroup meetings, and in this role will initiate and circulate draft meeting
agendas and provide meeting summaries.
B. Voluntary Participation; Designation of Party Representatives; Ability to

Set Meetings; Formation of Subcommittees: Participation in the Workgroup is
voluntary, and open to the public. As a consequence of this MOU, each Signatory
shall designate a representative as the primary contact for that Party on all
Workgroup activities. The designated representatives will constitute the
Workgroup Members. Workgroup Members agree to keep the Workgroup
informed of activities they are carrying out related to restoration efforts in the
Pilarcitos Creek watershed. As necessary, the Signatory from any Party can call a
meeting of the Signatories. At least one meeting of the Signatories will occur
during each calendar year to keep each Party informed of current events at the
policy recommendation and decision-making level. As necessary, the Workgroup
Members or Signatories can establish ad hoc subcommittees to conduct work on
2
behalf of the Workgroup. These ad hoc subcommittees would report back to the
Workgroup.
C. Meeting Schedules, Circulation of Agendas, and Meeting Minutes: The

Workgroup convenes approximately once every two months. Draft agendas and
meeting minutes will be circulated in advance to Workgroup Members for
comment before email distribution to the broader group. Draft minutes will be
finalized by adoption by Workgroup Members at the next meeting. Adopted
meeting minutes will be posted by the RCD on their website, making them
available to the public. If for whatever reason the RCD is unable or unwilling to
provide this service, new arrangements will be made to make these minutes
available to the public.
D. Workgroup Dispute Resolution: The intent of the Parties is that any dispute
should be resolved at the Workgroup Member level, if possible. However,
nothing contained herein shall be deemed to preclude any Party from seeking to
resolve a dispute between Parties by any other lawful means. If agreement on an
issue cannot be reached among the Workgroup Members, then any Party may
seek a more formal level of dispute resolution as described in this paragraph.
If any Party chooses to pursue formal dispute resolution, they may do so by

notifying the other Parties at the Signatory level in writing. This written
notification shall also include a statement of the issue and any pertinent
background material. The Parties will then convene a meeting of the Signatories
within 45 calendar days of this notification to review the issue. If the Signatories
cannot reach agreement, then the issue will remain unresolved, and each Party
will retain the right to resolve the dispute by any lawful means.
VI. Purpose, Conduct and Funding of Integrated Watershed Management Plan

A. Purpose of Integrated Watershed Management Plan: The purpose of the
IWMP is to set forth a strategy to achieve an ecologically sustainable watershed
that restores steelhead trout (while also considering other native species and
riparian communities) in the Pilarcitos Creek watershed while minimizing the
potential impacts to water supply and other beneficial uses, as described in the
Pilarcitos Creek IWMP Scope of Work. Given the diversity of
interests participating in the Workgroup, and the complexity of the issues
surrounding restoration in the Pilarcitos Creek watershed, a collaborative
Technical Team, led by an independent consultant, can play an important role by
generating data and analyses that are viewed as credible, unbiased, and can be
supported by the Workgroup Members.
B. Funding of Integrated Watershed Management Plan: The IWMP will be

funded by a $202,500 grant received by the San Francisco Public Utilities
Commission (SFPUC) from the State Water Resources Control Board’s 2005-
2006 Consolidated Grants Program, and an associated cost share contribution of
$67,500 from the SFPUC.
3
C. Preparation of Integrated Watershed Management Plan: The IWMP will
generally be prepared as follows:
1. Review the 1996 Plan and subsequent studies that have been produced
as a result of the 1996 Plan and confirm/update the watershed
characterization (e.g., hydrology, geomorphology, vegetation, wildlife)
and critical issues as described in the 1996 Plan (e.g., reduced
streamflow, degraded habitat, loss of riparian habitat, watershed
erosion and sedimentation, exotic and invasive vegetation, landowner
concerns).
2. Review and evaluate the status and recommendations from the 1996
Plan.
3. Establish specific objectives for the new planning effort that address
issues such as: a) habitat enhancement/restoration, b) reduced erosion
and sedimentation, c) removal/management of exotic and invasive
vegetation, d) increased native vegetation, e) improved water quality,
f) better flood management, g) stabilized creek banks, h) identification
of constraints and opportunities for protection and recovery of the
federally listed steelhead trout while incorporating current and future
water supply issues and important economic issues, i) development of
cost effective, stakeholder-supported alternative water supply projects
that could result in enhanced instream flows in the upper watershed
while minimizing loss of yield to consumers, j) development of
recycled water projects that may result in enhanced streamflow in
lower watershed, k) increased community collaboration.
4. Identify information gaps that potentially require additional

monitoring and/or studies.
5. Prepare draft IWMP that is based on the objectives in (3) above.
D. Oversight of Integrated Watershed Management Plan

The Workgroup will provide the oversight in the preparation of the IWMP.
VII. General Provisions of this MOU

A. Term: This MOU will expire in five years from the date of execution by all
the Parties unless extended by mutual consent of the Parties.
B. Amendments and Additional Signatories: This MOU may be amended at

any time with the unanimous approval of the Parties. Additional Parties may be
added at any time with the unanimous approval of the Parties.
4
C. Withdrawal: Any Party may withdraw from this MOU at any time by giving
30 days written notice to the other Parties. A Party that is dissatisfied with the
outcome of the dispute resolution process provided for in Section IIID may
withdraw. The MOU remains in effect for the remaining Parties.
D. Funding: Except as specifically described above, nothing herein alters the

existing authorities or responsibilities of any Party nor shall be considered as
obligating any Party in the expenditure of funds or the future payment of money or
providing services.
Implementation of this MOU by the signatory federal agencies is subject to the

Anti-Deficiency Act, 31 U.S.C. Section 1341, and the availability of appropriated
funds. This MOU is not intended and will not be construed to require the
obligation, appropriation, or expenditure of any money from the U.S. Treasury.
The signatories acknowledge that the federal signatories will not be required
under this MOU to expend any federal agency’s appropriated funds unless and
until an authorized official of that agency affirmatively acts to commit such
expenditures as evidenced in writing.
E. Construction of Terms: This MOU is for the sole benefit of the Parties and
shall not be construed as granting rights to any person other than the Parties or
imposing obligations on a Party to any person other than another Party.
F. Good Faith: Each Party shall use its best efforts and work wholeheartedly
and in good faith for the expeditious completion of the objectives of this MOU
and the satisfactory performance of its terms.
G. Governing Law: This MOU is made under and shall be governed by the
laws of the State of California.

Pilarcitos Integrated Watershed Management Plan: Pilarcitos Creek Restoration Workgroup

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Pilarcitos Integrated Watershed Management Plan: Pilarcitos Creek Restoration Workgroup

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December 31, 2007

Pilarcitos Integrated Watershed

Pilarcitos Creek Restoration Workgroup

Philip Williams & Associates, Ltd.

December 31, 2007

PWA REF. # 1884 T4

No other person or entity shall be entitled to rely on the services,

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2. INTRODUCTION AND PLANNING APPROACH 3

3. PLAN GOALS & OBJECTIVES 5

4. KEY WATERSHED MANAGEMENT ISSUES 8

5.1 PROJECT EVALUATION PROCESS 13

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Appendix A. Watershed Assessment Update

Appendix B. Workgroup Memorandum of Understanding

Table 1. Example Project Criteria Matrix

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Goal 2: Cost-effective, stakeholder-supported alternative water supply and water recycling

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Goal 4: Native vegetation is increased with prioritized attention to special-status plant

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Goal 6: Extensive community and stakeholder collaboration in watershed management

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4.1 INSTREAM FLOWS

4.1.1 Instream Flow Improvement Opportunities

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4.1.3 Grey Water Sources & Uses

4.2 ECOSYSTEM FUNCTIONS & PROCESSES

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4.2.1 Fish Passage & Instream Habitat

4.2.2 Watershed Erosion and Sedimentation

4.2.3 Channel Maintenance

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4.2.5 Control of Exotic and Invasive Vegetation

4.2.6 Lagoon Habitat

4.3 WATERSHED MANAGEMENT ISSUES

4.3.1 Community Engagement

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4.3.2 Beach Quality

4.3.3 Landowner Concerns

4.3.4 Landfill Issues

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5.1 PROJECT EVALUATION PROCESS

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5.1.1 Criteria for Project Priorities

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5.2.1 Arroyo Leon Ponds Rehabilitation

Project Implementation Lead: TBD

5.2.1.1 Project Summary

5.2.1.2 Project Benefits

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5.2.2 Stone Dam Flow Releases

Project Implementation Lead: TBD

Preliminary Cost Estimate: TBD