Swat Modeling Report

Neshanic River Watershed Restoration Plan
SWAT Modeling Analysis for the Neshanic River Watershed
Submitted by
Department of Chemistry and Environmental Science
New Jersey Institute of Technology
Newark, New Jersey
September 2010
Table of Contents
1. Background ................................................................................................................. 1
2. The Neshanic River Watershed ................................................................................. 1
3. Water Quality Criteria ............................................................................................... 3
4. Pollutant Source Characterization ............................................................................ 5
4.1. Point Sources ........................................................................................................ 6
4.2. Nonpoint Sources ................................................................................................. 6
4.2.1. Row Crop and Other Agricultural Lands ................................................. 6
4.2.2. Livestock .................................................................................................. 7
4.2.3. Wildlife ..................................................................................................... 8
4.2.4. Urban / Industrial Lands ........................................................................... 9
4.2.5. Household Sewage Treatment Systems (HSTS) .................................... 10
5. Modeling Process ...................................................................................................... 14
5.1. Introduction to SWAT ........................................................................................ 14
5.2. Input Data ........................................................................................................... 18
5.2.1. Digital Elevation Model Data ................................................................. 18
5.2.2. Soil Data ................................................................................................. 19
5.2.3. Land Use Data ........................................................................................ 21
5.2.4. Weather Data .......................................................................................... 23
5.2.5. Streamflow and Water Quality Data ...................................................... 23
5.2.6. Manure Content Data ............................................................................. 24
5.3. Model Setup........................................................................................................ 24
5.4. Baseline Scenario of Pollutant Sources and Management Practices .................. 26
5.5. Model Calibration and Validation ...................................................................... 29
5.5.1. Flow ........................................................................................................ 30
5.5.2. Water Quality Calibration ...................................................................... 32
5.5.3. Crop Yield Calibration ........................................................................... 35
6. Calibration Results and Discussion ......................................................................... 36
6.1. Flow Calibration ................................................................................................. 36
6.2. Sediment Calibration .......................................................................................... 41
6.3. Nutrient Calibration ............................................................................................ 47
6.4. Bacteria calibration ............................................................................................. 63
6.5. Crop Yield Calibration ....................................................................................... 70
7. Baseline Results ......................................................................................................... 72
7.1. Stream flow and Water Balance ......................................................................... 72
7.1.1. Watershed Streamflow Discharges......................................................... 72
7.1.2. Water Yields, Balance and Source Assessment ..................................... 74
7.2. Sediment Loading and Yields ............................................................................ 79
7.2.1. Watershed Sediment Loading................................................................. 79
I
7.3.
7.4.
7.5.
7.6.
7.7.
7.8.
7.2.2. Sediment Yields and Source Assessment ............................................... 80

Nitrogen Loading and Yields ............................................................................. 86
7.3.1. Watershed Nitrogen Loading ................................................................. 86
7.3.2. Nitrogen Yields and Source Assessment ................................................ 87
Phosphorus Loading and Yields ......................................................................... 92
7.4.1. Watershed Phosphorus Loading ............................................................. 92
7.4.2. Phosphorus Yields and Source Assessment ........................................... 93
Fecal Coliform Loading and Yields ................................................................... 98
7.5.1. Watershed Fecal Coliform Loading ....................................................... 98
7.5.2. Fecal Coliform Yields and Source Assessment...................................... 99
E. coli Loading and Yields ............................................................................... 103
7.6.1. Watershed E. Coli Loading .................................................................. 103
7.6.2. E. Coli Yields and Source Assessment................................................. 104
TMDL Targets .................................................................................................. 108
7.7.1. TMDL and Load Duration Curve ......................................................... 108
7.7.2. TMDL Targets of the Neshanic River watershed................................. 110
Critical Areas of Pollutant Loads Reduction .................................................... 120
8. BMP Scenarios ........................................................................................................ 121

8.1. Definition of BMP Scenarios ........................................................................... 121
8.1.1. Single-focus Management Scenarios ................................................... 121
8.1.2. Combinational Management Scenarios ................................................ 123
8.2. Load Reductions of BMP Scenarios................................................................. 127
8.2.1. Single-focus BMP Scenario Results ..................................................... 127
8.2.2. Combinational BMP Scenario Results ................................................. 128
9. Conclusions .............................................................................................................. 133
10. References ................................................................................................................ 135
Appendix A.
Management Schedules for Crops and Lawns .......................... 139
II
List of Tables
Table 4.1. Estimated manure production, fecal coliform and E. coli concentrations for
livestock .............................................................................................................................. 7
Table 4.2. Manure production, nutrient and pathogen loads from livestock in the
Neshanic River Watershed .................................................................................................. 8
Table 4.3. Estimated manure production, fecal coliform and E. coli concentrations for
wildlife ................................................................................................................................ 9
Table 4.4. Manure production, nutrient and pathogen loads from wildlife in the Neshanic
River Watershed.................................................................................................................. 9
Table 4.5. Estimated septic tanks and failures in Hunterdon County ............................... 10
Table 4.6. Pollutant loads from failing septic systems into streams ................................. 13
Table 5.1. Soils and area distributions .............................................................................. 20
Table 5.2. Land uses and are distributions* ...................................................................... 23
Table 5.3. Designed HRUs with cow and horse grazing .................................................. 27
Table 5.4. Designed HRUs with manure application ....................................................... 28
Table 5.5. Hydrology and sediment calibration parameters and their final calibrated
values ................................................................................................................................ 31
Table 5.6. Nutrient calibration parameters and their final calibrated values .................... 34
Table 5.7. Bacterial calibration parameters and their final calibrated values ................... 35
Table 6.1. Calibration results for flows at Reaville from 1997 to 2002 ........................... 38
Table 6.2. Daily flow calibration and validation at Reaville for each year ...................... 39
Table 6.3. Validation results for flows at Reaville from 2003 to 2008 ............................ 40
Table 6.4. Statistics of TSS loading calibration and validation at Reaville ...................... 44
Table 7.1. Base flow fractions from observed stream flow at the Reaville station .......... 73
Table 7.2. Water balance components on an annual average basis for the Neshanic river
watershed .......................................................................................................................... 75
Table 7.3. Average annual water yields of subbasins during 1997- 2008 ........................ 76
Table 7.4. Average annual yields of land uses in the Neshanic River Watershed ............ 77
Table 7.5. Average annual yields per unit area of land uses in the Neshanic River
Watershed ......................................................................................................................... 78
Table 7.6. Average annual water yields of land uses in subbasins during 1997- 2008 .... 79
Table 7.7. Average annual sediment yields of subbasins during 1997- 2008................... 81
Table 7.8. Average annual sediment yields of land uses in subbasins during 1997- 200885
Table 7.9. Average annual TN yields of subbasins during 1997- 2008............................ 88
III
Table 7.10. Average annual nitrogen yields of land uses in subbasins during 1997- 2008
........................................................................................................................................... 91
Table 7.11. Average annual TP yields of subbasins during 1997- 2008 .......................... 94
Table 7.12. Average annual phosphorus yields of land uses in subbasins during 19972008................................................................................................................................... 97
Table 7.13. Average annual fecal coliform yields of subbasins during 1997- 2008 ...... 100
Table 7.14. Average annual E. coli yields of subbasins during 1997- 2008................... 105
Table 7.15. Frequencies of TMDL exceedances and target reduction percentages........ 111
Table 7.16. Land classification for load reduction ......................................................... 120
Table 8.1. Definition of BMP scenarios ......................................................................... 126
Table 8.2. Reductions of sediment yields and loads under BMP scenarios ................... 129
Table 8.3. Reductions of TN yields and loads under BMP scenarios............................. 130
Table 8.4. Reductions of TP yields and loads under BMP scenarios ............................. 131
Table 8.5. Reductions of fecal coliform loads under BMP scenarios ............................. 132
Table 8.6. Reductions of E. coli loads under BMP scenarios ......................................... 133
IV
List of Figures
Figure 2.1. The Neshanic River watershed and study area ................................................. 2
Figure 4.1. Septic system areas in the Neshanic River Watershed ................................... 12
Figure 5.1. Nitrogen Processes Modeled in SWAT (USDA-ARS, 1999). ....................... 16
Figure 5.2. Phosphorus Processes Modeled in SWAT (USDA-ARS, 1999).................... 17
Figure 5.3. Elevation map of the Neshanic River Watershed ........................................... 18
Figure 5.4. Soils of the Neshanic River Watershed .......................................................... 19
Figure 5.5. Land use of the Neshanic River Watershed ................................................... 22
Figure 5.6. Delineation of the Neshanic River Watershed ............................................... 25
Figure 6.1. Annual observed and simulated stream flows at Reaville .............................. 37
Figure 6.2. Monthly observed and simulated stream flows at Reaville ............................ 37
Figure 6.3. Daily observed and simulated stream flows at Reaville during calibration
period ................................................................................................................................ 38
Figure 6.4. Filtered monthly base flows of observed and simulated stream flows at
Reaville ............................................................................................................................. 38
Figure 6.5. Observed and simulated and daily stream flows and precipitation during 1999
........................................................................................................................................... 39
Figure 6.6. Daily observed and simulated stream flows at Reaville during validation
period ................................................................................................................................ 40
Figure 6.7. Observed versus simulated stream flow duration curves at Reaville, 1997 to
2008................................................................................................................................... 41
Figure 6.8. Observed instantaneous stream flows, TSS concentrations and loads based on
water quality sampling at Reaville .................................................................................... 42
Figure 6.9. Observed instantaneous and daily flows loads and SWAT simulated daily
flows at Reaville on water quality sampling days ............................................................ 43
Figure 6.10. Simulated and USGS measured TSS concentrations at Reaville during the
calibration period .............................................................................................................. 43
Figure 6.11. Simulated and USGS measured TSS loads at Reaville during the calibration
period ................................................................................................................................ 43
Figure 6.12. Simulated and USGS measured TSS concentrations at Reaville during the
validation period ............................................................................................................... 44
Figure 6.13. Simulated and USGS measured TSS loads at Reaville during the validation
period ................................................................................................................................ 45
Figure 6.14. Simulated and project measured TSS concentrations at Reaville (N1) ........ 45
Figure 6.15. Simulated and project measured TSS concentrations at FN1 ...................... 45
Figure 6.16. Simulated and project measured TSS concentrations at SN1 ...................... 46
V
Figure 6.17. Simulated and project measured TSS concentrations at TN3 ...................... 46
Figure 6.18. Simulated and project measured TSS concentrations at TN3a .................... 46
Figure 6.19. Simulated and project measured TSS concentrations at UNT1 ................... 47
Figure 6.20. Simulated and project measured TSS concentrations at UNT2 ................... 47
Figure 6.21. Simulated and USGS measured ammonia nitrogen concentrations at Reaville
during the calibration period ............................................................................................. 48
during the validation period .............................................................................................. 48
Figure 6.23. Simulated and USGS measured nitrite + nitrate concentrations at Reaville
Figure 6.24. Simulated and USGS measured nitrite + nitrate concentrations at Reaville
Figure 6.25. Simulated and USGS measured TN concentrations at Reaville during the
Figure 6.26. Simulated and USGS measured TN concentrations at Reaville during the
Figure 6.27. Simulated and USGS measured MinP concentrations at Reaville during the
Figure 6.29. Simulated and USGS measured TP concentrations at Reaville during the
Figure 6.30. Simulated and USGS measured TP concentrations at Reaville during the
Figure 6.31. Simulated and project measured ammonia nitrogen concentrations at
Reaville (N1) ..................................................................................................................... 52
Figure 6.32. Simulated and project measured ammonia nitrogen concentrations at FN1 52
Figure 6.33. Simulated and project measured ammonia nitrogen concentrations at SN1 52
Figure 6.34. Simulated and project measured ammonia nitrogen concentrations at TN3 53
Figure 6.35. Simulated and project measured ammonia nitrogen concentrations at TN3a
........................................................................................................................................... 53
Figure 6.36. Simulated and project measured ammonia nitrogen concentrations at UNT1
........................................................................................................................................... 53
........................................................................................................................................... 54
Figure 6.38. Simulated and project measured nitrite +nitrate concentrations at Reaville
(N1) ................................................................................................................................... 54
VI
Figure 6.39. Simulated and project measured nitrite +nitrate concentrations at FN1 ...... 54
Figure 6.40. Simulated and project measured nitrite +nitrate concentrations at SN1 ...... 55
Figure 6.41. Simulated and project measured nitrite +nitrate concentrations at TN3 ...... 55
Figure 6.42. Simulated and project measured nitrite +nitrate concentrations at TN3a .... 55
Figure 6.43. Simulated and project measured nitrite +nitrate concentrations at UNT1 ... 56
Figure 6.44. Simulated and project measured nitrite +nitrate concentrations at UNT2 ... 56
Figure 6.45. Simulated and project measured TN concentrations at Reaville (N1) ......... 56
Figure 6.46. Simulated and project measured TN concentrations at FN1 ........................ 57
Figure 6.47. Simulated and project measured TN concentrations at SN1 ........................ 57
Figure 6.48. Simulated and project measured TN concentrations at TN3 ........................ 57
Figure 6.49. Simulated and project measured TN concentrations at TN3a ...................... 58
Figure 6.50. Simulated and project measured TN concentrations at UNT1 ..................... 58
Figure 6.51. Simulated and project measured TN concentrations at UNT2 ..................... 58
Figure 6.52. Simulated and project measured MinP concentrations at Reaville (N1) ...... 59
Figure 6.53. Simulated and project measured MinP concentrations at FN1 .................... 59
Figure 6.54. Simulated and project measured MinP concentrations at SN1 .................... 59
Figure 6.55. Simulated and project measured MinP concentrations at TN3 .................... 60
Figure 6.56. Simulated and project measured MinP concentrations at TN3a .................. 60
Figure 6.57. Simulated and project measured MinP concentrations at UNT1 ................. 60
Figure 6.58. Simulated and project measured MinP concentrations at UNT2 ................. 61
Figure 6.59. Simulated and project measured TP concentrations at Reaville (N1) .......... 61
Figure 6.60. Simulated and project measured TP concentrations at FN1 ......................... 61
Figure 6.61. Simulated and project measured TP concentrations at SN1 ......................... 62
Figure 6.62. Simulated and project measured TP concentrations at TN3 ........................ 62
Figure 6.63. Simulated and project measured TP concentrations at TN3a ....................... 62
Figure 6.64. Simulated and project measured TP concentrations at UNT1...................... 63
Figure 6.65. Simulated and project measured TP concentrations at UNT2...................... 63
Figure 6.66. Simulated and USGS measured fecal coliform concentrations at Reaville
Figure 6.67. Simulated and USGS measured fecal coliform concentrations at Reaville
Figure 6.68. Simulated and USGS measured E. coli concentrations at Reaville during the
VII
Figure 6.70. Simulated and project measured fecal coliform concentrations at Reaville
(N1) ................................................................................................................................... 66
Figure 6.71. Simulated and project measured fecal coliform concentrations at FN1 ....... 66
Figure 6.72. Simulated and project measured fecal coliform concentrations at SN1 ....... 66
Figure 6.73. Simulated and project measured fecal coliform concentrations at TN3....... 67
Figure 6.74. Simulated and project measured fecal coliform concentrations at TN3a ..... 67
Figure 6.75. Simulated and project measured fecal coliform concentrations at UNT1 .... 67
Figure 6.76. Simulated and project measured fecal coliform concentrations at UNT2 .... 68
Figure 6.77. Simulated and project measured E. coli concentrations at Reaville (N1) .... 68
Figure 6.78. Simulated and project measured E. coli concentrations at FN1 ................... 68
Figure 6.79. Simulated and project measured E. coli concentrations at SN1 ................... 69
Figure 6.80. Simulated and project measured E. coli concentrations at TN3 ................... 69
Figure 6.81. Simulated and project measured E. coli concentrations at TN3a ................. 69
Figure 6.82. Simulated and project measured E. coli concentrations at UNT1 ................ 70
Figure 6.83. Simulated and project measured E. coli concentrations at UNT2 ................ 70
Figure 6.84. Simulated and observed annual crop yields of corn and soybean. ............... 71
Figure 6.85. Simulated and observed annual crop yields of hay. ..................................... 71
Figure 7.1. Monthly stream flow and variation at the watershed outlet during 1997 2008
........................................................................................................................................... 73
Figure 7.2. Monthly TSS loads and variation at the watershed outlet during 1997-2008 80
Figure 7.3. Annual sediment yields from lands in each subbasin..................................... 82
Figure 7.4. Annual sediment yields from reaches in each subbasin ................................. 83
Figure 7.5. Source contributions for sediment average annual load ................................. 84
Figure 7.6. Contributions of sediment average annual yield from different land uses ..... 86
Figure 7.7. Monthly TN loads and variation at the watershed outlet during 1997-2008 .. 87
Figure 7.8. Annual nitrogen yields from lands in each subbasin ...................................... 89
Figure 7.9. Source contributions for TN average annual load .......................................... 90
Figure 7.10. Contributions of TN average annual yield from different land uses ............ 92
Figure 7.11. Monthly TP loads and variation at the watershed outlet during 1997-2008 93
Figure 7.12. Annual phosphorus yields from lands in each subbasin............................... 95
Figure 7.13. Source contributions for TP average annual load......................................... 96
VIII
Figure 7.14. Contributions of TP average annual yield from different land uses ............. 98
Figure 7.15. Monthly fecal coliform loads and variation at the watershed outlet during
1997-2008 ......................................................................................................................... 99
Figure 7.16. Annual fecal coliform yields from cattle direct deposits in subbasins ....... 101
Figure 7.17. Annual fecal coliform yields from failing septic systems in subbasins ..... 102
Figure 7.18. Source contributions of average annual load for fecal coliform ................ 103
Figure 7.19. Monthly E. coli loads and variation at the watershed outlet during 1997-2008
......................................................................................................................................... 104
Figure 7.20. Annual E. coli yields from cattle direct deposits in subbasins ................... 106
Figure 7.21. Annual E. coli yields from failing septic systems in subbasins ................. 107
Figure 7.22. Source contributions of average annual load for E. coli ............................ 108
Figure 7.23. TSS load duration curve at Reaville (N1) based on measured data ........... 112
Figure 7.24. TN load duration curve at Reaville (N1) based on measured data ............. 112
Figure 7.25. TP load duration curve at Reaville (N1) based on measured data ............. 113
Figure 7.26. Fecal coliform load duration curve at Reaville (N1) based on measured data
......................................................................................................................................... 113
Figure 7.27. E. coli load duration curve at Reaville (N1) based on measured data ........ 114
Figure 7.28. TSS load duration curve at Reaville (N1) based on simulation ................. 114
Figure 7.29. TN load duration curve at Reaville (N1) based on simulation ................... 115
Figure 7.30. TP load duration curve at Reaville (N1) based on simulation.................... 115
Figure 7.31. Fecal coliform load duration curve at Reaville (N1) based on simulation . 116
Figure 7.32. E. coli load duration curve at Reaville (N1) based on simulation .............. 116
Figure 7.33. TSS load duration curve at watershed outlet based on simulation ............. 117
Figure 7.34. TN load duration curve at watershed outlet based on simulation .............. 117
Figure 7.35. TP load duration curve at watershed outlet based on simulation ............... 118
Figure 7.36. Fecal coliform load duration curve at watershed outlet based on simulation
......................................................................................................................................... 118
Figure 7.37. E. coli load duration curve at watershed outlet based on simulation ......... 119
IX
1. Background
Federal guidance for Clean Water Act 319(h) grant funding calls for projects developing
watershed management plans to quantify pollutant sources and locate critical areas in the
watershed for prioritizing goals for restoration activity. In addition, projects should estimate load reductions for the proposed restoration activities. The Neshanic River Watershed is located in a suburban area of Central New Jersey. Land and water resources in
the watershed are adversely affected by rapid population growth, rampant urban development, and intense agricultural operations. Based upon numerous monitoring sources,
including the New Jersey Department of Environmental Protection (NJDEP) Ambient
Biomonitoring Network, the NJDEP/USGS water quality monitoring network, and the
Metal Recon Program, the Neshanic River and its branches are impaired for dissolved
oxygen, phosphorus, total suspended solids (TSS) and are on Sublists 5 of the New Jersey
Integrated Water Quality Monitoring and Assessment Reports (NJDEP, 2004; NJDEP,
2006; NJDEP, 2008a) for aquatic life, drinking water, and industrial water and Sublists 4
for recreation impairments. The watershed is also experiencing higher occurrences of
no/low stream flow in the Neshanic River in the late summer (Reiser, 2004). There is a
need for hydrological and water quality research of the Neshanic River Watershed to
make a comprehensive restoration plan that can better safeguard water resources, control
soil loss, and reduce phosphorus and pathogen loadings. Although there are a number of
studies of landscape, water budget, groundwater and surface water quality at the basin
scale for the Raritan River Basin that contains the Neshanic River Watershed, there is
none specifically investigating the hydrology and water quality restoration in the Neshanic River Watershed. A 319(h) Grant project funded by the New Jersey Department of Environmental Protection was initiated in 2006 for such purposes.
The objectives of this analysis are to evaluate current conditions for loading of sediment, nutrients (nitrogen and phosphorous), fecal coliform and E. coli, and then to evaluate the reduction of loads as a result of management alternatives and best management
practices to be implemented. The Soil and Water Assessment Tool (SWAT) was used to
support load assessment and reduction analysis with various management practices.
2. The Neshanic River Watershed

The Neshanic River Watershed (Figure 2.1) is located in Hunterdon County, Central New
Jersey, encompassing Raritan, Delaware, East Amwell and Flemington townships and is
a part of the Raritan River Basin. The Neshanic River is a tributary to the South Branch
of the Raritan River which drains to the Atlantic Ocean. The watershed restoration planning area is about 31 mi2 of the Neshanic River watershed, covering most of its drainage
area, including Walnut Brook, First, Second and Third Neshanic River and the Neshanic
River main branch immediately above the Back Brook entrance into the Neshanic River.
The study area consists of five Hydrological Unit Code (HUC) 14 areas, namely,
02030105030010, 02030105030020, 02030105030030, 02030105030040 on the west and
a potion of HUC 02030105030060 on the east.
Figure 2.1. The Neshanic River watershed and study area
The climate of the region is humid subtropical, with typically hot and humid summers and usually cold winters. According to weather data for the period 1955 2008, the
air temperatures during summers (June to August) show average high of 81 86 F (27
30 C) and lows of 55 61 F (13 16 C) with temperatures exceed 90 F (32 C) on
average 19 days each summer, though rarely exceed 100 F (38 C). The average high
temperatures during winters (December to February) are 37 41 F (3 5 C) and average lows are 19 29 F (-7 -5 C), but temperatures could, for brief interludes, be as
low as 10 20 F(-12 -7 C) and sometimes rise to 50 60 F (10 16 C). Spring and
autumn may feature wide temperature variations, ranging from chilly to warm, although
they are usually mild with lower humidity than summer.
The mean annual precipitation of the catchment area is about 1218 mm (19552008), falling on an average of 104 days a year, uniformly spread through the year.
Snowfall per winter season is about 5 30 inches (12 77 cm), but this varies from year
to year. During winter and early spring in some years the watershed can experience
nor'easters, which are capable of causing blizzards or flooding. There may also
experience drought and rain-free period for weeks. Hurricanes and tropical storms (such
as Hurricane Floyd in 1999) are rare. The annual mean evapotranspiration, groundwater
2
recharge, and runoff of the Neshanic River watershed are estimated to be 609 mm (23.96
inches), 133 mm (5.25 inches) and 401 mm (15.78 inches), respectively, according to the
a long-term water budget analysis for Raritan River Basin, which assumes that long-term
stream base flow is equivalent to long-term groundwater recharge (below the plant root
zone) except for the impacts of depletive and consumptive uses within the watershed
(NJWSA, 2000).
Like many other parts in New Jersey, this watershed had been experiencing rapid
suburbanization during the last two decades. Based on the land use/cover database compiled by the New Jersey Department of Environmental Protection (NJDEP), the percentage of the urban land in the watershed had increased from 16.6 percent in 1986 to 30.7
percent in 2002. The increases in urban land primarily came from agricultural land in the
watershed. While other land uses were relatively steady (forest: 20 percent; wetlands 10
percent; water 0.2 percent and barren 1.6 percent), the agricultural lands in the watershed
had decreased from 51.4 percent in 1986 to 36.4 percent in 2002.
The Neshanic River is classified as FW2-NT, or freshwater (FW) non-trout (NT).
FW2 refers to water bodies that are used for primary and secondary contact recreation;
industrial and agricultural water supply; maintenance, migration, and propagation of natural and established biota; public potable water supply after conventional filtration treatment and disinfection; and any other reasonable uses. NT means those freshwaters that
have not been designated as trout production or trout maintenance. NT waters are not
suitable for trout due to physical, chemical, or biological characteristics, but can support
other fish species (NJDEP, 2008a). The Neshanic River was considered to be one of the
worst water bodies in terms of overall water quality in the Raritan River Basin, as it had
either the highest concentrations of constituents or the highest frequency of not meeting
water quality standards for 13 of the 17 constituents (Reiser, 2004).
3. Water Quality Criteria

The results of this analysis are for planning use. As such, water quality goals were identified from available New Jersey surface water quality standards or from guidelines or recommended target levels. The designed use for the water bodies in the Neshanic River
Watershed is for total body contact recreational use during the recreation season. Indicators of water quality are constituents that are measured through analysis and used to estimate the status of a water body. The State of New Jersey has established surface water
quality standards and drinking water quality standards for some of these constituents and
the others assist with the assessment of the overall quality of the water (NJDEP, 2010b).
Total Suspended Solids
Total suspended solids (TSS) in surface waters occur primarily from storm water runoff,
stream bank and channel erosion, dead plant matter, plankton, and re-suspension of sediment into the water column. A high concentration of TSS negatively affects the surface
waters ecosystem and aesthetics. Fish and shellfish can be injured or killed from the TSS
by abrasive injuries, clogging gills and respiratory passages, and by blanketing the bot3
tom, killing eggs, young, and destroying spawning beds. The waters become cloudy and
the system can develop noxious conditions, reducing the aesthetic value of the waters.
Other pollutants, such as phosphorus and petroleum hydrocarbons, adsorb or bond to the
particles therefore magnifying the impact the solids have on the surface water quality.
TSS also interferes with the treatment processes for water purveyors. The surface water
criterion is 25 mg/L in trout waters and 40 mg/L in non-trout waters. The Neshanic River
is a non-trout river.
Total Phosphorus
Total phosphorus in surface water is a key nutrient for stimulating excessive growth of
aquatic plants and algae, resulting in the eutrophication of water bodies. Phosphorus is a
common element in igneous minerals and sediments and is found both in solution and
adsorbed to particulates. Orthophosphate is the soluble form of phosphorous and is readily available for uptake by aquatic plants and algae. Although phosphorus occurs in surface waters naturally through weathering of minerals and sediment, human influence has
increased its presence. The use of orthophosphorus on lawns, gardens, and agricultural
lands leads to its presence in runoff. Phosphorus also enters streams from wastewater
treatment plant effluent. The surface water quality criterion for phosphorus is 0.1 mg/L,
and this criterion shall not be exceeded in any stream unless it can be demonstrated that
total phosphorus is not a limiting nutrient and will not render the waters unsuitable for the
designated uses. A second surface water quality criterion of 0.05 mg/L exists for lakes,
reservoirs, and streams at the point of entry to these water bodies. The NJDEP recently
adopted an amendment to the NJ surface water criterion for total phosphorus to allow watershed-based criteria in addition to site-specific criteria.
Ammonia plus Organic Nitrogen
Ammonia plus organic nitrogen, also called Total Kjeldahl Nitrogen or TKN, represents
the reduced portion of total nitrogen in a stream. When a compound is reduced it gains an
electron by bonding with hydrogen. Ammonia in natural waters results from either direct
discharge, such as wastewater discharges and animal wastes, or the decomposition of nitrogenous organic matter, such as detritus (dead plant matter). Ammonia is highly soluble
in water and high concentrations are a concern for water purveyors because of increased
treatment costs. Ammonia and organic nitrogen are both oxygen consumers and indicators of ecosystem health. No water quality criterion exists for ammonia plus organic
nitrogen.
Nitrate plus Nitrite
Nitrate plus nitrite represents the oxidized form of nitrogen in the stream. When a compound is oxidized it loses an electron (by adding oxygen in this case). They are found in
surface waters as a result from wastewater discharge, runoff from land application of fertilizers, and ground water polluted by fertilizers. Nitrate concentrations in surface waters
tend to be higher than nitrite because nitrite rapidly oxidizes to nitrate. They are a primary nutrient for rooted aquatic plants and algae and are a concern for water users. The
drinking water standard for nitrate is 10 mg/L and nitrite is 1 mg/L. The surface water
4
criterion for nitrate is the same as the drinking water standard and there is no criterion
for nitrite. Nitrate is less toxic than either ammonia or nitrite, but can cause methemoglobinemia (blue baby syndrome) in small children and fish.
Total Nitrogen
Total nitrogen is the sum of organic nitrogen, ammonia, and nitrate plus nitrite. The target criterion for total nitrogen was set to 10 mg/L for this planning. Note that this criterion was selected for panning purpose only and is not meant to be used to set any discharge limitation on any point source or identify any water quality violation, but is used
simply as a benchmark for achieving improved water quality conditions from the current
observed level.
Fecal Coliform
An indication of the sanitary quality of a water body is determined from fecal coliform
bacteria counts. Fecal coliform bacteria are used as an indicator of fecal contamination
and of the possible existence of waterborne enteric pathogens. This is because coliform
bacteria are derived from the digestive tract of mammals. Sources for fecal coliform in
surface water are untreated wastewater, failing septic systems, and animal waste. High
fecal coliform counts can render the effected water body unsuitable for swimming. In
New Jerseys previous surface water quality standards two surface water quality criteria
were adopted that concentrations should not exceed: 1) a geometric mean of 200 colonies per 100 milliliters, and 2) 400 colonies per 100 milliliter in more than 10 percent
of total samples collected in a 30 day period. This standard was still applied in this planning.
E. coli
Recently, non-point sources have surpassed point sources as the major source of fecal
contamination to surface waters. This creates a need to identify the source of fecal contamination from non-point pollution. Fecal coliform measurements do not provide information on the specific source of pollution, such as animal versus human. To address this
need the USGS and NJDEP have begun monitoring for other indicator organisms such as
Enterococcus bacteria, Escherichia coli (E. coli), and bacteriophages (viruses that infect
bacteria) specific to humans or using DNA testing to determine species. In 2004, the fecal
coliform standard in New Jersey for FW2 waters was replaced by a water quality standard for E. coli. E. Coli levels shall not exceed a geometric mean of 126/100 ml or a
single sample maximum of 235/100 ml. The Neshanic River violated both the previous
coliform standard and the new E. coli standard. Because the goal of this planning is to
meet current water quality standards, best management practice (BMP) selection and
placement will be based on the E. coli standard.
4. Pollutant Source Characterization

In order to assess the loading conditions in the watershed for sediment, nutrients, fecal
coliform and E. coli, an inventory of contributing sources was necessary.
5
4.1. Point Sources

According to the regulation in the United States, generally point sources include municipal wastewater (sewage), industrial wastewater discharges, municipal separate storm
sewer systems (MS4) and industrial stormwater discharges (Public Law 100-4, 1987).
These facilities are required to obtain National Pollution Discharge Elimination System
(NPDES) permits or state/local permits. According to NJDEPs point source surface discharges GIS data layer, there are only two permitted industrial point sources (Suburban
Sunoco Inc, and Hess Station 30333) discharging treated petroleum products cleanup
wastewater to the Neshanic River via a unnamed tributary and storm sewer, located near
the watershed boundary with East Amwell Township, both at latitude 40 26' 29.7" and
longitude 74 51' 26.5". Since their discharge levels were small, no point source was considered in the plan.
4.2. Nonpoint Sources
Nonpoint source (NPS) pollution comes from diffuse sources that cannot be identified as
entering the water body at a single location. These sources generally involve land activities that contribute pollution to streams during wet weather events. Rain or snow-melt
moves over and through the ground where pollutants have accumulated, transports the
contaminants, and deposits them into nearby water bodies. Bacterial NPS pollution is
generated by both human and non-human (animal) sources via land use activities. Nonpoint sources are predominately agriculture and non-regulated residential area that are
outside storm sewer systems service.
Typical non-point sources of nutrients and pathogens in the Neshanic River Watershed include, but are not limited to:
Fertilizer and manure application to croplands

Livestock grazing on pastureland
Livestock with direct access to streams
Wildlife
Urban land activities
Leaking/failing septic systems
4.2.1. Row Crop and Other Agricultural Lands

While many of the water quality problems were attributed to the rapid urban development, agriculture was still an important source of water pollution in the watershed. The
Neshanic River watershed had the highest percentage of agricultural lands among all watersheds in the Raritan River Basin. Therefore, controlling agricultural nonpoint source
runoff is important for achieving the overall water quality goals in this watershed. The
Neshanic River watershed was recognized as one of the priority watersheds to implement
agricultural BMPs to improve water quality because of its relatively poor water quality
and high percentage of agricultural lands (NJWSA, 2002).
Area-specific information of cropping activities was gathered that included crop
frown, types of tillage, fertilizers and pesticides used. Corn and soybeans are the predo6
minant crops in the watershed and a small amount of farmland grows wheat/rye, hay and
timothy. Nitrogen fertilizer to corn lands is primarily applied as anhydrous ammonia liquid fertilizer. Nitrogen fertilizer is also applied to rye, hay, timothy, pasture and orchard
lands. Phosphorus is usually applied corn, soybean and other crop lands in granular form
blended in various combinations with other nutrients. There is no spatial location data for
tillage. However, reduced tillage is common for all crop lands in the watershed. For specific operation schedules refer to tables in Appendix A.
4.2.2. Livestock
Livestock in the watershed include mainly beef cattle and horse. Manure from livestock
was considered as a potential source of nutrients, fecal coliform and E. coli. Despite the
lack of distribution information of livestock operations in the watershed, animal live tock
numbers by county were obtained from the National Agricultural Statistics Service
(NASS)s 2007 agricultural census, and were proportioned to the Neshanic watershed
based on total agricultural areas. Cow (beef and dairy cattle) and horse are selected as
representative livestock since they generate much more manure amounts than other animals. It was estimated that there were 560 cows and 408 horses in the Neshanic River
watershed in average during the simulation period.
The number of animals, the amount of manure produced by each animal, and the
concentrations of nutrients and bacteria in the manure were used to calculate the impact
of livestock (Table 4.1). The manure productions, fecal coliform contents and loading
rates of cows and horses were calculated from reported daily manure production and fecal coliform amounts from standards for typical livestock (ASAE, 2003). E. coli contents
of all animals were calculated as 62.5% of the contents of fecal coliform of corresponding animals (IDNR, 2006).
Table 4.1. Estimated manure production, fecal coliform and E. coli concentrations for livestock
Animal
Cow
Horse
Manure
production
(kg/d/animal)
20.880
22.950
Fecal coliform
in fecal matter
(cfu/kg feces)
4.83E+09
1.80E+07
E. coli
in fecal matter
(cfu/kg feces)
3.02E+09
1.13E+07
Fecal coliform
loading rate
(cfu/d/animal)
1.01E+11
4.14E+08
E. coli
loading rate
(cfu/d/animal)
6.30E+10
2.59E+08
The manure production, nutrient and pathogen loads from livestock in the Neshanic
River Watershed are listed in Table 4.2, in which dry manure productions were calculated
based on the values for typical mature beef cow and horse in ASAE (2003). The nutrient
loads were calculated based on the content percentages in dry manure given in SWAT
fertilizer database.
Table 4.2. Manure production, nutrient and pathogen loads from livestock in the Neshanic
River Watershed
Animal
Number
Cow
Horse
560
408
Manure
production
(kg/d)
11692.800
9363.600
Dry
Fecal
E. coli
manure
coliform
load
production
load
(cfu/d)
(kg/d)
(cfu/d)
1713.600
5.64E+13 3.53E+13
2754.000
1.69E+11 1.06E+11
Min-N
(kg/d)
17.136
16.524
Min-P
(kg/d)
6.854
2.754
Org-N
(kg/d)
51.408
38.556
Org-P
(kg/d)
11.995
8.262
4.2.3. Wildlife
Wildlife in the Neshanic River Watershed include many animals, including but not limited to deer, raccoons, rodents, geese, and ducks, most of them difficult to inventory.
Although New Jerseys Landscape Project maps rare and imperiled wildlife habitats,
there is no inventory for density distribution of common wildlife at the county level in
New Jersey. Hunting reports in previous years were utilized to quantify wildlife population and densities. Nutrient and fecal contributions by wildlife in the Neshanic River Watershed were estimated. Deer and goose were considered as the representatives. New Jerseys white-tailed herd is a major component of the landscape throughout all but the most
urbanized areas of the state, and the estimated annual populations during 1984 and 2006
range from 120,000 to 200,000, or 13.7 to 22.9 per square mile (NJDEP, 2008b). Approximately, 64,000 deer are harvested annually from about 5,000 square miles of deer
range in the Garden State. Each square mile yields an average of 4 antlered bucks and 8
antlerless deer (NJDEP, 2010a). The average density of deer in the Neshanic River Watershed was assumed to be 20 deer per square mile across the whole watershed.
Canada geese are grazers that have a clear preference for tender, mowed and fertilized turf grass, although they also feed heavily on small grains such as corn and soybeans during the fall and winter. They prefer to feed in large open areas with few obstructions that give the birds a 360-degree view of potential predators. Giant Canada geese
differ from seasonally migrating interior Canada geese. The NJDEPs Division of Fish
and Wildlife conducts a breeding population survey each spring, when only resident species are present in New Jersey because the migrating geese already have traveled to
northern breeding grounds. The population of resident Canada geese in New Jersey
was estimated at approximately 98,000, or 11.2 per square mile (NJDEP, 2010c). Suburban development often leads to an increase in lawns, recreational fields and other grassy
areas, all viewed as appealing habitat by Canada geese. Therefore, as development continues in New Jersey, it is likely that the population of resident geese will continue to increase. To reflect the seasonal immigration of interior Canada geese during winter and
the hatching and growing of young residential Canada geese during spring and summer,
the average goose density in the watershed was assumed to be double of resident geese,
about 22 geese per square mile throughout the year.
The numbers of these animals and amount of manure produced by each type, along
with nitrogen, phosphorus, fecal coliform, and E. coli concentrations were used to calculate loads from wildlife (Table 4.3, Table 4.4). Manure productions of deer and goose
8
were taken from the Salt Creek Watershed TMDL study (WHPA, 2004). Daily fecal coliform loading rates of deer and goose were from TMDL for Pathogens in Beeds Lake
Franklin County, Iowa (IDNR, 2006). The nutrient loads were calculated based on the
content percentages in dry manure given in SWAT fertilizer database. This was achieved
by assuming deer and goose have the same dry manure percentages and nutrient concentrations as goat and duck, respectively.
Table 4.3. Estimated manure production, fecal coliform and E. coli concentrations for wildlife
Animal
Density
(#/mi2)
Deer
Goose
20
22
Manure pro- Fecal coliform in

duction
fecal matter
(kg/d/animal)
(cfu/kg feces)
0.772
0.163
6.48E+08
3.01E+11
E. coli in
fecal matter
(cfu/kg feces)
Fecal coliform
loading rate
(cfu/d/animal)
4.05E+08
1.88E+11
5.00E+08
4.90E+10
E. coli in
fecal matter
loading rate
(cfu/d/animal)
3.13E+08
3.06E+10
Table 4.4. Manure production, nutrient and pathogen loads from wildlife in the Neshanic
River Watershed
Dry
Fecal
Manure
E. coli load
manure
coliform
Animal Number production
(cfu/d)
production
load (cfu/d)
(kg/d)
(kg/d)
Deer
608
469.376
148.827
3.04E+11 1.90E+11
Goose
668
108.884
30.685
3.27E+13 2.05E+13
Min-N
(kg/d)
Min-P
(kg/d)
Org-N
(kg/d)
Org-P
(kg/d)
1.935
0.706
0.446
0.245
3.274
0.767
0.744
0.276
4.2.4. Urban / Industrial Lands

Runoff from urban and industrial areas can potentially contribute nutrients and bacteria to
streams and rivers. The nutrients and bacteria can come from such sources as pet feces,
urban wildlife, sanitary sewer cross-connections, and deficient solid waste collection. To
assess the impact of the urban runoff, the built-up areas are classified into four subcategories and the loading rates for each of these divisions can be calculated based on
published accumulation rates (USEPA, 2000). Unfortunately, similar accumulation rates
are not available for E. coli.
E. coli is a subset of fecal coliform, meaning measurement of fecal coliform includes all measurement of E. coli, along with other pathogens. The amount of E. coli will
be lower than the amount of fecal coliform in manure. Therefore, the low-end of the
range for the fecal coliform accumulation rates can be used as estimation for E. coli. The
accumulation rates for fecal coliform range from 1.8x108 2.1x1010 cfu/ac/day (USEPA,
2000). If the accumulation rate for E. coli in urban areas is designated as 1.8x108
cfu/ac/day, assuming E. coli is 62.5% of fecal coliform, accumulation rate for fecal coliform is about 2.88 x 108 cfu/ac/day.
4.2.5. Household Sewage Treatment Systems (HSTS)

Household sewage treatment systems (e.g., septic systems) provide the potential to deliver nutrient and bacteria loads to surface waters due to system failures caused by improper
maintenance, malfunctions, and/or close proximity to a stream.
The 2000 census data and GIS layers were utilized to estimate failing septic systems in the watershed. From GIS analysis, there are 1508 and 1188 households located in
sewer service areas and non-sewer service areas, respectively (Figure 4.1). Note that even
within sewer service areas, there are households utilizing septic systems. The 2000 census indicates that the household sizes of Raritan, Delaware and east Amwell were 2.81,
2.72 and 2.80, respectively.
No study clearly estimates how many septic systems fail or do not properly function in the watershed. Generally, the failures of septic systems are attributed to older
homes. However, maintenance also affects septic failure rates. The failure rate of these
units can be estimated from their construction dates, also determined from the 2000 census data. Three categories of units were considered: before 1970, 1970-1989, and after 1989.
The rates of failure were assumed to be 40%, 20%, and 5%, respectively. These rates have
been used in Virginia for the development of TMDLs and were backed up by studies done in
that area that found 30 % of all septic tanks were either failing or not functioning at all
(VDEQ, 2002). Using these rates and the number of septic systems in Hunterdon County, we
estimated the number of failing systems in Table 1. Considering 10 years have passed the
2000 census, the failure rate of septic systems is estimate as 30% to account for more failures
of houses built after year 2000 in the Neshanic river watershed.
Table 4.5. Estimated septic tanks and failures in Hunterdon County

Structure age
Pre 1970
1970-1989
Post 1989
Total
Number of units
20,410
16,902
7,720
45,032
Failure rate (%)

40
20
5
26.5
Number failed
8164
3380
386
11930
The nutrient and pathogen loads from failed septic systems were defined as the
amount per day reaching streams, and calculated obtained based on the following assumptions:
One septic system per household for those located in non-sewer service areas and those
located in sewer service areas but do not discharge wastewater to sewer collection systems;
Assume 20 percent of households located in sewer service areas utilize septic systems;
Average number of persons served by each system: 2.8;
Failure percentage: 30%;
Septic system effluent discharge rate of 70 gallons/person/day
Average pollutant concentrations of septic sewage at the point when it reaches the stream
was not available, so the concentrations in septic tank effluents were used, 40 mg/l TN,
10
12 mg/l TP, 1 x 106 cfu/100mL fecal coliform, and 6.3 x 105 cfu/100mL E. coli, re
spectively.
Daily loads discharged by a failing septic system: 29.674 g/d TN, 8.902 g/d TP, 7.42 x
109 cfu/d fecal coliform, and 4.67 x 109 cfu/100mL E. coli, respectively.
A further assumption was made after calibration testing: only septic systems within 200
meters distance of streams can have failing tank effluents reach streams, and only 20%
effluent loads enter streams due to the removal on pathways.
Based on the above assumptions, as shown in Table 4.6, the total loads of effluents
from failing septic systems and entering streams in the watershed were estimated as 0.973
kg/d TN, 0.292 kg/d TP, 2.433E+11cfu/d fecal coliform, and 1.533E+11 cfu/d E. coli.
Note that, the nonpoint source loads presented in the Section Pollutant Source Characterization are estimates at overland deposit sites. They are most likely higher than the
loads received by the streams, because nutrient and pathogen loads would probably be
reduced from detrimental environmental conditions as it moved from the septic tank to
the stream. However, there is evidence that E. coli can survive and even reproduce in the
natural environment given the right environmental conditions (WHPA, 2004).
11
Figure 4.1. Septic system areas in the Neshanic River Watershed
12
Table 4.6. Pollutant loads from failing septic systems into streams
Subbasin
Area
(ha)
Number
of septic
systems
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
Total
599.026
278.54
437.737
293.92
134.592
448.664
387.066
298.953
175.867
234.944
355.807
387.757
225.388
252.104
268.884
355.547
263.871
287.215
253.395
206.806
403.386
264.972
515.315
313.962
251.694
7895.412
190
305
111
77
61
152
418
157
2
72
17
216
121
71
33
30
56
53
44
9
299
19
98
45
40
2696
Failing
systems
close to
streams
18
5
7
2
0
16
14
22
0
0
1
6
10
6
5
1
5
4
1
1
13
1
14
8
4
18
13
TN
load
(kg/d)
TP
load
(kg/d)
0.107
0.030
0.042
0.012
0.000
0.095
0.083
0.131
0.000
0.000
0.006
0.036
0.059
0.036
0.030
0.006
0.030
0.024
0.006
0.006
0.077
0.006
0.083
0.047
0.024
0.973
0.032
0.009
0.012
0.004
0.000
0.028
0.025
0.039
0.000
0.000
0.002
0.011
0.018
0.011
0.009
0.002
0.009
0.007
0.002
0.002
0.023
0.002
0.025
0.014
0.007
0.292
Fecal
coliform
load
(cfu/d)
2.671E+10
7.419E+09
1.039E+10
2.967E+09
0.000E+00
2.374E+10
2.077E+10
3.264E+10
0.000E+00
0.000E+00
1.484E+09
8.902E+09
1.484E+10
8.902E+09
7.419E+09
1.484E+09
7.419E+09
5.935E+09
1.484E+09
1.484E+09
1.929E+10
1.484E+09
2.077E+10
1.187E+10
5.935E+09
2.433E+11
E. coli
load
(cfu/d)
1.683E+10
4.674E+09
6.543E+09
1.869E+09
0.000E+00
1.496E+10
1.309E+10
2.056E+10
0.000E+00
0.000E+00
9.347E+08
5.608E+09
9.347E+09
5.608E+09
4.674E+09
9.347E+08
4.674E+09
3.739E+09
9.347E+08
9.347E+08
1.215E+10
9.347E+08
1.309E+10
7.478E+09
3.739E+09
1.533E+11
5. Modeling Process
The watershed model named Soil and Water Assessment Tool (SWAT) version 2005 was
applied to the Neshanic River Watershed to evaluate hydrology and sediment, nutrients
and bacteria loadings by simulating the influence of topographic, soil, land use, and climatic condition on stream flow and sedimentation. The application involved sensitivity,
calibration, validation, and water, sediment, nutrients, and bacteria balance analyses. The
calibrated SWAT was then applied to evaluate the effects of various best management
practices for reducing nonpoint source pollutant loadings.
5.1. Introduction to SWAT
SWAT is a continuous, daily time-step spatially distributed hydrological river basin scale
model that simulates the water, sediment, nutrient, chemical and bacteria transport in a
watershed resulting from the interaction of weather, soil properties, stream channel characteristics, vegetation and crop growth, and land management practices, and calculates
various pollutant loads from landscape and point sources (Arnold et al., 1994; Neitsch et
al., 2005). It delineates a watershed into hydrologic response units (HRUs) that consist of
specific land use, soil and slope characteristics to represent spatial heterogeneity in terms
of land cover, soil type and slope class within a watershed. The model estimates relevant
hydrologic responses such as evapotranspiration, surface runoff and peak rate of runoff,
groundwater flow, sediment and pollutant yields for each HRU to the changing climate
and land use conditions. ArcSWAT is an ArcGIS extension that provides a graphic user
interface for the SWAT2005 model. SWAT integrates field-scale BMPs being implemented within a watershed and evaluates their water quality benefits at sub-watershedand watershed-scale over a long period of time. This model has be widely applied to estimate water quality impacts of BMPs (Fohrer et al., 2002; Gitau et al., 2006; Santhi et
al., 2001b; Tripathi et al., 2003) and effectiveness of alternative regulatory instruments
(Qiu and Prato, 1999; Whittaker et al., 2003).
The hydrologic cycle in SWAT is based on the following water balance equation:
SWt SW0 Rday Qsurf Ea Wseep Qqw i

t
(1)
i 1
where, t is the index of time step (days), SWt is the final soil water content (mm water)
by the end time step t, SW0 is the initial soil water content (mm water), Rday is the
amount of precipitation in day i (mm water), Qsurf is the amount of surface runoff in day
i (mm water), Ea is the amount of evapotranspiration in day i (mm water), Wseep is the
amount of water entering the vadose zone from the soil profile in day i (mm water), and
Qqw is the amount of return flow in day i (mm water). SWAT can estimate surface runoff
using two methods: the SCS curve number procedure (USDA-SCS, 1972) and the Green
& Ampt infiltration method (Green and Ampt, 1911). In this study, the SCS curve num-
14
ber method was chosen to estimate surface runoff. The SCS curve number (CN) is defined by:
Qsurf
( Rday 0.2S ) 2
Rday 0.8S
(2)
where, S is the retention parameter (mm), S 25.4(1000 / CN 10) . The SCS curve
number (CN) for the day is a function of the soils permeability, land use and antecedent
soil water conditions. SCS defines three antecedent moisture conditions: 1-dry (wilting
point), 2-average moisture, and 3-wet (filed capacity). The moisture condition 1 curve
number is the lowest value that the daily curve number can be assumed in dry conditions.
The curve numbers under moisture conditions 1 (CN1) and 3 (CN3) are calculated from
the moisture condition 2 (CN2) by:
CN1 CN 2
20(100 CN 2 )
(100 CN 2 exp(2.533 0.0636(100 CN 2 )))
CN 3 CN 2 exp(0.00673(100 CN 2 ))
(3)
(4)
Peak runoff rate is computed using a modification to the Rational formula (Kuichling, 1889) or using the SCS TR-55 method (USDA-SCS, 1986). Lateral subsurface flow
is computed using the Sloan et al. (1983) kinematic storage model and ground-water flow
using empirical relations. Routing of in-channel runoff is based on the variable storage
coefficient method (Williams, 1969) and flow is computed using Mannings equation
(Chow, 1959) with adjustments for transmission losses, evaporation, diversions, and return flow as described in Arnold et al. (1995). Flow routing in reservoirs is based on water balance and user provided measured or targeted outflow.
Sediment yield is computed using the Modified Universal Soil Loss Equation
(MUSLE) (Williams and Berndt, 1977) expressed in terms of runoff volume, peak flow,
and Universal Soil Loss Equation (USLE) (Wischmeier and Smith, 1978) factors. Sediment routing in the channel is based on Bagnolds (1977) stream power concept, as modified by Williams (1980), for bed degradation and sediment transport. Bed degradation is
adjusted with USLE soil erodibility and cover factors, and deposition is based on particle
fall velocity. Reservoir sediment routing is based on a simple continuity equation on volumes and concentrations of inflow, outflow, and reservoir storage. The modified universal soil loss equation (Williams, 1995) adopted in SWAT is given out in the following
mass balance equation:
sed 11.8(Qsurf q peak areahru ) 0.56 KUSLE CUSLE PUSLE LSUSLE CFRG
(5)
where, sed is the sediment yield on a given day (metric tons), Qsurf is the surface runoff
volume (mm H2O/ha), qpeak is the peak runoff rate (m3/s), areahru is the area of the HRU
(ha), KUSLE is the USLE soil erodibility factor (0.013 metric ton m2 hr/(m3-metric ton
cm)), CUSLE is the USLE cover and management factor, PUSLE is the USLE support prac15
tice factor, LSUSLE is the USLE topographic factor and CFRG is the coarse fragment factor.
The nitrogen processes modeled by SWAT and the various pools of nitrogen in the
soil are shown in Figure 5.1 (Arnold et al., 1998; Neitsch et al., 2005). Plant use of nitrogen is estimated using the supply and demand approach (Williams et al., 1984). Daily
plant demand is a function of plant biomass and biomass N concentration. Available nitrogen in the soil (root depth) is supplied to the plant. When demand exceeds supply,
there is a nutrient stress. Masses of NO3-N contained in runoff, lateral flow and percolation are estimated as products of the volume of water and the average concentration of
nitrate (NO3-N) in the soil layer. Organic N transport with sediment is calculated with a
loading function developed by McElroy et al. (1976) and modified by Williams and Hann
(1978) for application to individual runoff events. The loading function estimates daily
organic N runoff loss based on the concentration of organic N in the top soil layer, the
sediment yield, and an enrichment ratio (that is, the ratio of organic N in sediment to organic N in soil and typically ranging from two to four). The phosphorus processes modeled by SWAT and the various pools of phosphorus in the soil are depicted in Figure 5.2
(Neitsch et al., 2005). Plant use of phosphorus is estimated using the supply and demand
approach similar to nitrogen. The loss of dissolved phosphorus in surface runoff is based
on the concept of partitioning pesticides into solution and sediment phases as described
by Leonard and Wauchope (1980). The amount of soluble P removed in runoff is predicted using labile P concentration in the top 10 mm of the soil, the runoff volume and a
phosphorus soil partitioning factor (that is, the ratio of P attached to sediment to P dissolved in soil water and typical values range from 100 to 175 depending on the soil). Sediment transport of P is simulated with a loading function as described in organic N
transport (Santhi et al., 2001a).
Instream nutrient dynamics have been incorporated into SWAT (Ramanarayanan et
al., 1996) using the kinetic routines from an instream steady-flow water quality model,
QUAL2E (Brown and Barnwell, 1987).
Figure 5.1. Nitrogen Processes Modeled in SWAT (USDA-ARS, 1999).
16
Figure 5.2. Phosphorus Processes Modeled in SWAT (USDA-ARS, 1999).
The SWAT microbial sub-model for predicting pathogen loadings in surface and
groundwater at watershed and basin scale was developed by Sadeghi and Arnold (2002).
Its approach involves developing a comprehensive and flexible bacteria submodel that
can allow simultaneous risk evaluation of nutrients, pathogens and sediment loadings associated with various land management practices in water catchments. The model has
been tested in a watershed in Missouri (USA) for E. coli and fecal coliform (Baffaut and
Benson, 2003). Parajuli (2007) has also evaluated and applied the SWAT microbial submodel to watersheds in Kansas (USA). This sub component of SWAT simulates the survival of enteric organisms as two different populations: (i) nonpersistent microorganisms
and (ii) persistent microorganisms, such as Cryptosporidium species and E. coli (Jamieson et al., 2004). Persistent bacteria are characterized by slower die-off rates in the natural environment (Coffey et al., 2007; Foppen and Schijven, 2006). The rationale for this
approach is that the population of persistent bacteria like E. coli and Cryptosporidium
may initially be low in comparison to less persistent bacteria (i.e. fecal coliform). However, because of more rapid die-off rates for less persistent bacterial species, the population of more persistent bacteria would likely comprise a greater proportion of the total
remaining pathogens (Sadeghi and Arnold, 2002). The impact of persistent pathogens is
thus evaluated based on population densities. Recent enhancements in relation to microbial risk assessment include bacteria transport routines in sediment and in-stream (Sadeghi and Arnold, 2002). In reality, bacterial transport is associated with both dissolution in
overland flow and sorption onto sediments. It is unknown if this sorption occurs on the
land, during runoff events, or during in-stream processes. However, significant uncertainty in modeling both bacterial partitioning and sediment transport has caused most models
to treat bacteria transport as being entirely associated with dissolution in surface runoff
(Chin et al., 2009; Coffey et al., 2010).
17
5.2. Input Data
In order to run the SWAT model, various input data are needed. Many of the data are
readily available in the form of geographic data sets (elevation, soil and land use) from
public sources; and others such as cropping practices, tillage, fertilizer application, waste
and stormwater management are locally dependent and are not readily available.
ArcSWAT, the ArcGIS interface of SWAT2005, was used to delineate the watershed and
process SWAT input files (Winchell et al., 2009).
5.2.1. Digital Elevation Model Data
Topography was defined by a digital elevation model (DEM) that describes the elevation
of any point in a given area at a specific spatial resolution. A 10 m DEM was obtained for
the watershed from NJDEP. The geography and topological relief of the watershed are
shown in Figure 5.3. This grid file was used by ArcSWAT to delineate subwatersheds
and to analyze the drainage patterns of the land surface terrain. A 1:24K stream network
obtained from NJDEP was used to set the stream network for the delineation. Subbasin
parameters such as slope gradient, slope length of the terrain, and stream characteristics
such as channel length, width and slope were calculated from the DEM. There are 5593,
2020 and 282 ha of watershed areas falling into the slope ranges of 0-2%, 2-5% and
above 5%, which are 70.84%, 25.59%, and 3.57% of the total area, respectively.
Figure 5.3. Elevation map of the Neshanic River Watershed
18
5.2.2. Soil Data
SWAT model requires different soil textural and physicochemical properties such as soil
texture, available water content, hydraulic conductivity, bulk density and organic carbon
content for different layers of each soil type. A digital soil survey layer (Figure 5.4) was
created for the watershed from the Soil Survey Geographic (SSURGO) Database for
Hunterdon County, New Jersey, which is obtained from Natural Resources Conservation
Service (NRCS), United States Department of Agriculture. Excluding water and ROPF
(rough broken land, shale), fifty two soil types were classified in the watershed according
to soil composition and slopes. Table 5.1 lists the types of soils and their area distributions. Major soils types in the watershed are: Penn channery silt loam with 6 to 12 percent slopes, eroded (16.63%), Penn channery silt loam with 2 to 6 percent slopes
(16.44%), Bucks silt loam, 2 to 6 percent slopes (8.07%), Reaville silt loam, 2 to 6 percent slopes (6.81%), Chalfont silt loam, 2 to 6 percent slopes(4.70%), Rowland silt loam,
0 to 2 percent slopes, frequently flooded (4.52%), Hazleton channery loam, 6 to 12 percent slopes, eroded (3.81%), and Abbottstown silt loam, 2 to 6 percent slopes (3.58%).
Figure 5.4. Soils of the Neshanic River Watershed
19
Table 5.1. Soils and area distributions

musym
AbrA1
AbrB1
BhnA2
BhnB2
BoyAt1
BucB2
BucC21
ChcA1
ChcB1
ChcC21
ChfB1
CoxA1
CoxBb
HdyB1
HdyC21
HdyD
HdyDb
HdyEb
KkoC
KkoD
LbmB2
LbmC21
LbtB1
LdmB2
LegB2
LegC1
LegD
LemB1
MonB2
NeeB2
NehB2
NehCb
NehDb
NehEb
PeoB2
PeoC21
PeoD
PepB2
PepC21
QukB2
QukC21
QupC21
ROPF
RarAr2
RarB2
RedB2
Soil Name
Abbottstown silt loam, 0 to 2 percent slopes
Abbottstown silt loam, 2 to 6 percent slopes
Birdsboro silt loam, 0 to 2 percent slopes
Birdsboro silt loam, 2 to 6 percent slopes
Bowmansville silt loam, 0 to 2 percent slopes, frequently
flooded
Bucks silt loam, 2 to 6 percent slopes
Bucks silt loam, 6 to 12 percent slopes, eroded
Chalfont silt loam, 0 to 2 percent slopes
Chalfont silt loam, 2 to 6 percent slopes
Chalfont silt loam, 6 to 12 percent slopes, eroded
Chalfont-Quakertown silt loams, 0 to 6 percent slopes
Croton silt loam, 0 to 2 percent slopes
Croton silt loam, 0 to 6 percent slopes, very stony
Hazleton channery loam, 2 to 6 percent slopes
Hazleton channery loam, 6 to 12 percent slopes, eroded
Hazleton channery loam, 12 to 18 percent slopes
Hazleton channery loam, 6 to 18 percent slopes, very stony
Hazleton channery loam, 18 to 40 percent slopes, very
stony
Klinesville channery loam, 6 to 12 percent slopes
Klinesville channery loam, 12 to 18 percent slopes
Lansdale loam, 2 to 6 percent slopes
Lansdale loam, 6 to 12 percent slopes, eroded
Lansdowne silt loam, 2 to 6 percent slopes
Lawrenceville silt loam, 2 to 6 percent slopes
Legore gravelly loam, 2 to 6 percent slopes
Lehigh silt loam, 2 to 6 percent slopes
Mount Lucas silt loam, 2 to 6 percent slopes
Neshaminy gravelly loam, 2 to 6 percent slopes
Neshaminy silt loam, 2 to 6 percent slopes
Neshaminy silt loam, 6 to 12 percent slopes, very stony
Penn channery silt loam, 2 to 6 percent slopes
Penn channery silt loam, 6 to 12 percent slopes, eroded
Penn channery silt loam, 12 to 18 percent slopes
Penn-Bucks complex, 2 to 6 percent slopes
Penn-Bucks complex, 6 to 12 percent slopes, eroded
Quakertown silt loam, 2 to 6 percent slopes
Quakertown silt loam, 6 to 12 percent slopes, eroded
Quakertown-Chalfont silt loams, 6 to 12 percent slopes,
eroded
Rough broken land, shale
Raritan silt loam, 0 to 3 percent slopes, rarely flooded
Raritan silt loam, 3 to 8 percent slopes
Readington silt loam, 2 to 6 percent slopes
20
Acres
94.20
709.69
7.95
48.16
Percent
0.47
3.58
0.04
0.24
153.06
0.77
1601.24
200.30
143.03
932.21
577.50
417.51
24.84
35.11
308.73
755.20
174.98
8.07
1.01
0.72
4.70
2.91
2.10
0.13
0.18
1.56
3.81
0.88
228.71
1.15
113.93
0.57
264.83
214.15
63.37
66.12
11.81
5.71
92.41
92.39
54.17
1.99
15.48
7.89
24.74
6.31
7.96
35.39
3262.31
3299.31
373.27
537.57
118.70
442.38
106.70
1.33
1.08
0.32
0.33
0.06
0.03
0.47
0.47
0.27
0.01
0.08
0.04
0.12
0.03
0.04
0.18
16.44
16.63
1.88
2.71
0.60
2.23
0.54
214.42
1.08
355.24
265.12
68.37
165.74
1.34
0.34
0.84
0.30
RedC21
RehA1
RehB1
RehC21
RepwA
RepwB
RorAt
Water
Readington silt loam, 6 to 12 percent slopes, eroded

Reaville silt loam, 0 to 2 percent slopes
Reaville silt loam, 2 to 6 percent slopes
Reaville silt loam, 6 to 12 percent slopes, eroded
Reaville wet variant silt loam, 0 to 2 percent slopes
Reaville wet variant silt loam, 2 to 6 percent slopes
Rowland silt loam, 0 to 2 percent slopes, frequently
flooded
Water
59.90
21.70
1350.82
164.68
304.02
330.66
0.11
6.81
0.83
1.53
1.67
1.79
897.05
4.52
12.26
0.06
5.2.3. Land Use Data
Land use significantly affects soil erosion, runoff, and evapotranspiration processes in a
watershed. The 2002 land use/cover data obtained from NJDEP was used for SWAT
modeling. NJDEP land use/cover data used a modified Anderson Land Classification system. The land uses in this watershed were classified into six broad land use categories
including agriculture, barren, forest, urban, water and wetlands, and 50 subcategories using a 4-digital land use classification codes. Since the NJDEP land use classification did
not distinguish the specific uses of agricultural lands, two rounds of agricultural land use
inventories throughout the watershed were conducted during the period 2007-2008 to
identify the crops and agricultural activities in agricultural lands. There are 21 types of
land uses/covers identified including residential areas (high, medium, medium-low and
low densities), other urban type areas (commercial, institutional and transportation), forests (deciduous, evergreen and mixed), wetlands (forested, non-forested and mixed), and
agricultural lands (corn, soybean, rye, timothy, regular hay, pasture, orchard and other
agriculture) (Figure 5.5). Table 5.2 lists the types of land uses and their area distributions.
21
Figure 5.5. Land use of the Neshanic River Watershed
22
Table 5.2. Land uses and are distributions*

Land use
Residential-High Density
Residential-Medium Density
Residential-Med/Low Density
Residential-Low Density
Commercial
Institutional
Transportation
Agricultural Land-Generic
Corn
Soybean
Rye
Hay
Timothy
Pasture
Orchard
Forest-Deciduous
Forest-Evergreen
Forest-Mixed
Wetlands-Forested
Wetlands-Non-Forested
Wetlands-Mixed
Water
Code
URHD
URMD
URML
URLD
UCOM
UINS
UTRN
AGRL
CORN
SOYB
RYE
HAY
TIMO
PAST
ORCD
FRSD
FRSE
FRST
WETF
WETN
WETL
WATR
Acres
96.18
216.70
382.03
4894.54
290.34
456.68
163.54
351.82
1846.58
1846.64
346.39
757.32
1681.05
888.51
112.65
3038.28
208.22
914.05
1089.34
6.56
204.67
53.99
Percent
0.48
1.09
1.92
24.66
1.46
2.30
0.82
1.77
9.30
9.30
1.75
3.82
8.47
4.48
0.57
15.31
1.05
4.61
5.49
0.03
1.03
0.27
* 2002 land use data with 2007-2008 updates
5.2.4. Weather Data
SWAT requires daily meteorological data that can either be read from a measured data
set or be generated by a weather generator model. The weather data at the Flemington
weather station that is just outside of the watershed boundary from NOAA's National
Climate Data Center were utilized to set up the SWAT model. The historical weather data
include the precipitation, maximum and minimum temperature during 1960-2008, solar
radiation and relative humidity during 1960-2004 in the Flemington weather station. The
weather generator in SWAT can automatically utilize historical data to interpolate and fill
the gaps due to missing data.
5.2.5. Streamflow and Water Quality Data
Daily stream flow in the Neshanic River has been monitored at the intersection between
Reaville Road and the Neshanic River since 1930 by the U.S. Geological Survey
(USGS). These daily streamflow data were obtained from USGS and used for flow calibration and validation. Water quality data including instantaneous discharge, TSS, nutrients, E coli and Fecal coliform, are available at the same site with two to five sam23
plings a year in some years since 1979. Additional water quality monitoring was conducted at seven locations in the watershed including the USGS station and six other sites
in the tributaries of Neshanic River (Figure 2.1) during 2007 to 2008 through the restoration plan project: biweekly surface water sampling from June -November 2007 (12
events), additional bacteriology sampling three times in June, July and August 2007 (9
events), biological sampling once in early summer of 2007 (1 event), wet weather surface
water sampling three times between June -November 2008 (3 events). The instantaneous
stream flows and TSS concentrations obtained through these samplings were utilized to
validate the model.
5.2.6. Manure Content Data
The fertilizer database in SWAT contains nutrient content data of many commercial fertilizers and manures of several types of animals. Each manure type in the fertilizer database used by SWAT contains an associated bacteria count for persistent (e.g. E. coli) and
less persistent bacteria (e.g. Fecal coliforms). Values required by the database are the
bacteria content per gram of dry manure. However, these required data are not recorded
in the database and need users definition. These inputs were estimated based on the values reported in literature as described in the previous section on pollutant source characterization.
5.3. Model Setup
The model setup involved five steps: data preparation, subbasin delineation, HRU definition, parameter sensitivity analysis, and calibration and validation. The required spatial
datasets were projected to the same projected coordinate system defined by NJDEP: StatePlane_New_Jersey_FIPS_2900 _Feet, which is a transverse mercator projection based
on NAD 1983 for New Jersey. The DEM was used to delineate the watershed and to analyze its drainage patterns. NJDEP stream network for the watershed was imported and
superimposed onto the DEM to accurately delineate the location of streams. The land
use/cover data were reclassified into SWAT land cover/plant types. A look-up table was
created to identify the SWAT code for the different categories of land use/cover on the
map as per the required format. The required soil attributes were extracted from the
SSURGO database to create a user soil table used in SWAT. A look-up table was created
to link the locations of soil types in the soil map to the soil attributes in user soil table in
SWAT.
Based on DEM and the stream network the watershed and subwatersheds were delineated by further outlet and inlet definition, watershed outlets selection, and definition
and calculation of subbasin parameters. For the stream definition the threshold based
stream definition option was used to define the minimum size of the subbasin. The
ArcSWAT interface allows the user to fix the number of subbasins by deciding the initial
threshold area. The threshold area defines the minimum drainage area required to form
the origin of a stream. 25 subbasins were delineated in the watershed (Figure 5.6), where
the sampling sites for water quality monitoring were selected as subbasin outlets, as
SWAT outputs simulated flow and loading values at subbasin watersheds.
24
During set up of the SWAT model the distribution of hydrological response units
(HRUs) within the watershed are determined based on user criteria. HRUs are unique
combinations of land use, soil and slope which allow the model to reflect differences in
evapotranspiration and other hydrologic conditions across the watershed. Three slope
classes were considered for Neshanic River watershed, 0-2%, 2-5% and >5%. The large
number of HRUs needs to be reduced to simplify the input to SWAT model while still the
major differences among subwatersheds are accounted for. To achieve this, area percentage thresholds for HRU definition were set at 1%, 20% and 25% for land use, soil and
slope, respectively. This forced the model to create HRUs comprised of combinations of
land use, soils and slope meeting the minimum threshold areas for each subbasin. As a
result, a land use in a subbasin covering less than 1% of the total area for that subbasin, or
a soil type comprising less than 20% of the land use area in that subbasin, or a slope classification comprising less than 25% of the soil area in that subbasin, would be ignored
and reclassified as a more dominant combination. Using these thresholds 625 individual
HRUs were defined for the 25 subbasins delineated in the watershed.
Figure 5.6. Delineation of the Neshanic River Watershed
25
5.4. Baseline Scenario of Pollutant Sources and Management Practices
A scenario details the management options in the manageable land uses including lawn
managements in urban lands and crop management in agricultural lands, such as tillage,
fertilization applications and harvest. The baseline scenario was developed through a series of interviews and meetings with farmers and natural resource professionals in the watershed. The baseline scenario is characterized with modest N and P commercial fertilizer
applications and reduced tillage for agricultural lands. Cattle and horse manures were assumed to be applied to corn lands at standard rates. The pesticide application was ignored. Tillage operations include: minimum (chisel/disk) plows for corn, soybean and
rye, and 6-year rotation moldboard/disk/hallow plows for timothy, hay and pasture lands.
Agricultural general lands (AGRL) were modeled as 2-year rotation of corn and soybean.
Orchards, forests, and wetlands were modeled using their default SWAT schedules.
5.4.1.1. Agricultural Management Practices

The schedules of management practices for various land uses are given in Appendix A.
Operations for agricultural lands normally involve tillage, fertilization, planting, and
harvest. A specific date was assigned to each operation. Although the dates of actual activities may span over a large range, specific dates are required for a schedule in SWAT.
Note that estimate of operation dates may lead to big difference between the simulated
and observed daily times series of stream flows and pollutant loads. However, good comparable results can be obtained at the monthly level.
It was assumed that cattle and horses grazed on pasture lands from May to October
after which they were hay supplemented in the winter pastures until the end of March.
Distributions of livestock among HRUs in a subbasin were assigned to reflect the relative
areas of cows and horses in that subbasin as close as possible (Table 5.3). Either cows or
horses were allowed on a HRU but not both. A GIS layer of livestock distribution parcels
were created based on consultation of farmers. Cow and horse densities were assumed to
be the same across the whole watershed, being 4.5 cows/ha and 1.7 horses/ha, respectively. Daily dry matter intakes were taken as 2.5% of mature body weights (Rinehart, 2006).
Commercial fertilizer application amounts for crops were set according to common
practice recommendations and farmer consultation. Land application of manure helps to
reduce or eliminate the need for commercial fertilizers. It can be applied in four different
ways: 1) surface broadcast followed by disking 2) broadcast without incorporation 3) injection under the surface, or 4) irrigation. It was difficult to get data about how much and
which areas were applied to manure in the watershed. Cow and horse manure application
rates were set to 45 Mg/ha (based on N requirement) (Santhi et al., 2006) and applied to
corn lands only with incorporation in Spring. With these manure application rates, the
maximum corn land areas receiving cow and horse manures were 47 and 38 ha, respectively. In total, only 11.5% percentage of corn lands might be applied with the available
manure stored during the livestock housing period. Cow and horse manures were assigned to corn land HRUs to match the spatial distribution pattern of livestock (
26
Table 5.4). The small amount of remaining manure storage was assumed to be well managed and not modeled with SWAT.
Table 5.3. Designed HRUs with cow and horse grazing
Land
use
PAST
PAST
PAST
PAST
PAST
PAST
PAST
PAST
PAST
PAST
PAST
PAST
PAST
PAST
PAST
PAST
PAST
PAST
PAST
PAST
PAST
PAST
PAST
PAST
PAST
PAST
PAST
PAST
PAST
PAST
PAST
PAST
PAST
PAST
PAST
PAST
PAST
PAST
PAST
PAST
PAST
Subbasin
3
3
5
5
6
6
6
7
7
10
10
10
11
12
12
12
12
13
13
13
13
14
14
15
16
16
16
17
17
18
20
20
22
22
23
23
23
24
24
25
25
HRU
60
61
104
105
128
129
130
154
155
227
228
229
262
298
299
300
301
318
319
320
321
351
352
368
392
393
394
423
424
442
492
493
539
540
567
568
569
590
591
624
625
Acres
9.98
23.08
3.48
9.07
16.31
30.39
25.70
10.01
4.27
19.40
12.01
13.20
13.22
7.34
8.97
4.25
6.50
1.48
2.36
1.99
2.94
4.62
8.70
8.92
75.37
44.97
48.93
34.84
32.87
49.17
38.30
33.85
59.55
21.00
43.24
54.36
19.00
37.07
17.79
21.42
12.50
Soil
ChfB
ChfB
ChcB
RarAr
PeoB
PeoC2
RehB
PeoB
PepB
PeoB
PeoC2
RepwB
PeoB
PeoC2
PeoC2
PeoD
PeoD
LbmC2
LbmC2
PeoC2
RehB
PeoC2
PeoC2
QukB
PeoB
PeoC2
PeoC2
PeoB
PeoC2
RedB
PeoB
RehB
RehB
RehB
AbrB
PeoC2
PeoC2
PeoB
RehB
ChcA
HdyC2
27
Slope
2.57
1.21
0.92
0.57
1.00
0.96
0.74
0.77
0.39
0.76
1.16
0.80
0.45
1.50
3.23
3.32
1.31
1.72
2.44
3.13
2.85
2.63
1.24
0.62
0.87
2.93
1.24
0.44
0.54
0.95
0.61
0.58
1.21
2.65
1.09
1.19
2.76
0.68
0.92
0.71
1.02
Cow
grazing
Horse
grazing
yes
yes
yes
yes
yes
yes
yes
yes
yes
yes
yes
yes
yes
yes
yes
yes
yes
yes
yes
yes
yes
yes
Yes
Yes
Yes
Yes
yes
yes
yes
yes
yes
yes
yes
yes
yes
yes
yes
yes
yes
yes
yes
Table 5.4. Designed HRUs with manure application

Land
use
CORN
CORN
CORN
CORN
CORN
CORN
CORN
CORN
CORN
Subbasin
8
9
12
16
17
18
20
24
25
HRU
171
197
285
380
416
433
483
582
612
Acres
9.41
18.58
8.01
27.92
9.41
46.95
12.95
39.78
27.92
Soil
RehB
RepwA
PeoB
PeoC2
PeoC2
BucB
PeoC2
QukB
QukB
Slope
0.36
0.50
2.71
2.95
0.65
0.66
3.01
0.73
0.87
Cow manure
Horse
manure
yes
yes
yes
yes
yes
yes
yes
yes
yes
5.4.1.2. Cattle Direct Deposit

Access to streams allows livestock to input manure directly into the streams. It was assumed that most horse owners did not allow their horses access for fear of disease, so no
access was input for horses. Since no accurate information about fence placement was
available, it was estimated that on 20% of pasture lands, cattle would be able to access
stream directly and would only spend 2% of grazing time in the stream. This estimation is
based on rough judgment and bacteria calibration testing.
5.4.1.3. Wildlife Deposit

The nutrient and bacteria loads associated with deer and geese were taken onto accounted
though continuous grazing operations. Deer were assumed to living on various forest
lands, while geese on low-density residential, commercial, institutional and transportation
urban area lawns. The deer and goose manure deposit rates on these lands were estimated
by dividing densities in the whole watershed by the fractions of their total habitat areas
relative to watershed area.
Fecal coliform and nutrient loads that are deposited by wildlife directly into the
streams can be treated as direct point source loadings in SWAT model. However, it is
very difficult to estimate the amount of manure directly deposited by these animals into
the water. Furthermore, direct deposition into stream from wildlife is a natural activity
hardly to be dealt with any BMPs. The direct deposits in the stream from wildlife were
not specified in this study.
5.4.1.4. Urban Runoff

Sediment and nutrients on both pervious and impervious areas from urban lands are simulated with default loading rates in SWAT. However, the SWAT model currently does
not simulate the accumulation of bacteria on impervious areas and their subsequent washoff by storm runoff. Two approaches may be adopted to remedy this situation. One is to
estimate an average bacteria concentration for all urban storm runoff using wet weather
28
data published in the NPDES permit annual reports and wet weather urban runoff data,
and code it into the SWAT model to calculate the approximated average bacteria loads
carried by urban runoff. Baffaut (2006) utilized this method and calculated the average
fecal coliform concentration of urban runoff in Little Sac River Watershed was to be 549
238 colonies/100 ml. A second approach is to assume all bacteria are deposited through
grazing on pervious lands. The second method was adopted in this study such that only
bacteria deposits on lawns by the representative wildlife, geese, were simulated. This approximation is reasonable considering low density residential areas are the dominant type
of urban lands in the Neshanic River Watershed.
5.4.1.5. Failing Septic Systems

Failing septic systems are normally be regarded as nonpoint sources, which can be simulated in SWAT through continuous fertilization management operation (Coffey et al.,
2010) or as aggregate point sources (Parajuli, 2007). In this report, the effluents from
failing septic systems in a subbasin were aggregated to obtain point source loading input
to the main river network. Once total nitrogen and phosphorus loads were aggregated for
each subbasin, they were partitioned into organic and mineral forms using the following
relationships from Northern Virginia Planning District Commission (1979) and adopted
within SWAT. Total nitrogen loads consist of 70 percent organic nitrogen and 30 percent
mineral (nitrate). Total phosphorus loads were divided into 75 percent organic phosphorus and 25 percent orthophosphate. Failing septic systems and cattle direct manure deposits to streams within each subbasin were aggregated into a point source with monthly
flows and pollutant loadings for SWAT modeling.
5.4.1.6. Groundwater Contamination

According to the 2007 groundwater quality report by New Jersey Geology Survey
(NJGS, 2007) , the concentration ranges of TN, Dissolved P (Orthophosphate) in the Neshanic River Watershed were 0.3-4.38 mg/L and 0.02-0.06 mg/L, respectively. SWAT
can simulate the leaching process of nitrogen and its concentrations in aquifers, but it assumes that phosphorus and bacteria cannot be leached beyond the top soil layer. Dissolved phosphorus concentrations in groundwater need to be input manually, which were
set to be 0.02 mg/L evenly across the Neshanic River Watershed.
5.5. Model Calibration and Validation
Calibration is the process of obtaining an optimal agreement between the model prediction and an observed data set. Parameters of the model are adjusted iteratively to improve
predicted values against the actual observed values for stream flow, sediment, nutrients
and bacteria. Once calibration is complete, validation is performed to evaluate the accuracy of the model to predict values from an observational data set different from the calibration observational data set used. Poor model validation results may imply possible
model calibration inaccuracies. The SWAT model for Neshanic River Watershed was
calibrated with the crop management schedules under the baseline scenario, which reflect
the existing crop management conditions. The scenario was developed through a series of
interviews and meetings with farmers and natural resource professionals in the watershed.
29
The baseline scenario is characterized by minimum tillage (chisel plow and disk plow)
and typical fertilizer applications in the area. To accommodate the 6-year rotation for hay
and pasture standings, the calibration and validation periods were both set to 6 years, as
1998-2002 and 2003-2008, respectively. The simulation started at 1997, and hence a 6year warm-up period was used to establish proper initial parameter values for the SWAT
modeling before the calibration period.
It is important to note that the SWAT model is built with state-of-the-art components with an attempt to simulate the processes physically and realistically as possible.
Most of the model inputs are physically based (that is, based on readily available information). SWAT is not a parametric model with a formal optimization procedure (as
part of the calibration process) to fit any data. Instead, a few important variables that are
not well defined physically such as runoff curve number and Universal Soil Loss Equations (USLE) cover and management factor (C factor) may be adjusted to provide a better fit. SWAT has been widely used in the United States and other countries (Borah and
Bera, 2004). Borah and Bera (2004) have extensively reviewed the various nonpoint
source pollution models and their applications and indicated that SWAT is found to be
sound and suitable for long-term continuous simulations especially in agricultural watersheds.
5.5.1. Flow
Calibration was performed for annual, monthly and daily simulated flows using observed
flows from the Reaville USGS streamflow gage station at the intersection of Reaville
Road and the Neshanic River which is marked as N1 (USGS station 01398000 near the
outlet of subbasin 12) in Figure 2.1. There is an area of about 6,493 ha that drains to the
gage station.
The parameter sensitivity analysis was done using the Latin-Hypercube OneFactor-At-a-Time (LH-OAT) approach embedded in ArcSWAT for the whole catchment
area. Twenty six hydrological parameters that affect stream flows were tested for sensitivity analysis for the simulation of stream flows in the study area. Default lower and upper bound parameter values were used. For details of all hydrological parameters refer to
the ArcSWAT Interface for SWAT users manual (Winchell et al., 2009).
The calibration process was done manually to ensure that not only simulated stream
flows matched the observed stream flows but also their properly split (filtered) surface
runoffs and base flows were matched. VIZSWAT version 1.1 (Baird, 2007) was used to
separate base flow and runoff for the observed and simulated daily stream flows at Reaville which utilizes an automated digital filter technique comparable with Nathan and
McMahon (1990), and Arnold and Allen (1999).
Calibration parameters adjusted for surface runoff were mainly curve number, soil
evaporation compensation factor, maximum canopy storage, available water capacity of
the soil layer, hydraulic conductivity in the main channel alluvium, and surface runoff
lag. The parameters adjusted for base flow proportioning were base flow alpha factor,
groundwater revap coefficient, groundwater delay, and deep aquifer percolation coeffi30
cient. These parameters were adjusted within the reported ranges (Table 5.5). Surface runoff was calibrated until average observed and simulated surface runoffs were within
15% and coefficient of determination (R2) and Nash-Sutcliffe efficiency (NSE) greater
than 0.5, as far as possible. Similarly, base flow was calibrated until the simulated base
flow is within 15% of the observed base flow, and surface runoff was continually verified
as the base flow calibration variables also affect surface runoff. Detailed calibration procedures for SWAT model and the definitions of various calibration parameters are described by Neitsch et al. (2005) and Santhi et al. (2001a).
Table 5.5. Hydrology and sediment calibration parameters and their final calibrated values
Model
Parameter
process
Flow
Cn2
Esco
Canmx
Sol_Awc
Ch_K2
Surlag
Alpha_Bf
GW_Revap
GW_Delay
Rchrg_DP
Sediment
USLE_C
USLE_P
Ch_cov
Ch_erod
SPCON
SPEXP
Model
range
Curve number
25%
Soil evaporation compensation factor 0 1
Maximum canopy storage (mm H2O) 0 10
Available water capacity of the soil
25%
layer (mm H2O/mm soil)
Hydraulic conductivity in the main
0 150
channel alluvium (mm/hr)
Surface runoff lag coefficient
0 100
Base flow alpha factor (days)
01
Groundwater revap coefficient
0.02 0.2
Groundwater delay time (days)
0 100
Deep aquifer percolation fraction
01
Value used
Description
Minimum value for the cover and

0.003
management factor for the land cover 0.45
Universal Soil Loss Equation support
practice factor
Channel cover factor
Channel erodibility factor
Linear factor for channel sediment
routing
Exponential factor for channel sediment routing
+1.5%
0.40
5
+25%
4
1
0.11
0.2
20
0. 4
Pasture, hay, timothy:
0.003, rye: 0.03, other
croplands: 0.20
0.1 1
01
0 to 1
0.0001
0.01
0.5
0.01
1.0 1.5
0.001
1.5
The calibration and validation were carried out by graphical comparison and statistics. Several statistics including the mean, mean relative error (D), standard deviation,
coefficient of determination (R2) and Nash-Sutcliffe efficiency (NSE) coefficient (Nash
and Sutcliffe, 1970) were used to evaluate the model predictions against the observed
values. The R2 value is an indicator of strength of relationship between the observed and
simulated values. The Nash-Sutcliffe simulation efficiency indicates how well the plot of
observed versus simulated value fits the 1:1 line. The simulation efficiency indicates the
models ability to describe the probability distribution of the observed results. If the R2
and NSE values are less than or very close to 0.0, the model prediction is considered unacceptable or poor. If the values are 1.0, then the model prediction is perfect. Ramanarayanan et al. (1997) suggests that model prediction is acceptable if R2 > 0.5 and NSE >
0.4. Mean relative error (D), coefficients of determination (R2) and Nash-Sutcliffe efficiency (NSE) are calculated by following equations.
31
D (S O ) O
(6)
2
(Oi O )( Si S )
R 2 n i 1
n
(Oi O )2 (Si S )2
i 1
i 1
NSE 1
(7)
(S
i 1
n
Oi ) 2
(Oi O )2
(8)
i 1
where, Oi is the observed value, O is the mean observer value, Si is the simulated value,
S is the mean simulated value.

5.5.2. Water Quality Calibration
After hydrology was sufficiently calibrated, water quality calibration was performed for
total suspended solids, nitrogen components, mineral and total phosphorus, fecal coliform
and E. coli bacteria. Continuous records of water quality monitoring data were not available for calibration in the Neshanic River Watershed. However, grab sample data were
available for some years since 1979 for the USGS monitoring station at Reaville. Usually
4 samples per year (1 per quarter) were taken for pollutants, and bacteria were sampled 5
times during the 30-day summer period from July to August. Due to limited available observed water quality data, a robust calibration and validation procedure is not possible for
pollutants. Limited model calibrations were carried out by comparing simulated in-stream
concentration time series with the available observed concentrations with graphic method. The additional data obtained at the seven sites during 2007-2008 through the water
quality monitoring program of the Neshanic restoration plan project were used for validation purpose. The objective was to best simulate the observed data for individual samples,
as well as to obtain modeling output within the same ranges as the observed data. Because of the simplified implementation of instream kinetics in SAWT, coupled with uncertainty in the specification of boundary conditions, particularly for point source loads, it
cannot be expected that all observations will be reproduced in the modeling. However,
the general trend should be replicated.
Note that daily concentrations were computed from daily average loads and flows
output from SWAT, while observed concentrations were actually instantaneous values
mostly only one during a sampling day. For a few days when two samples were collected
within a day, observed pollutant concentration in a day was simply approximated as the
flow weighted average of samples at a site during that day.
Careful considerations were given to verify the processes related to sediment and
nutrients. Instream suspend solids result from the interaction of upland loading and
32
scour/deposition processes in the stream channels. The model parameters related to sediment (Table 5.5) were set based on expertise and experience from previous studies
(Neitsch et al., 2005; Santhi et al., 2001a). Model parameters verified for sediment (for
upland processes) calibration were the Universal Soil Loss Equations land cover and
management factor (C factor) and support practice factor (P factor). Parameters verified
for channel sediment routing processes were channel cover factor, channel erodibility
factor, linear factor and exponential factors for channel sediment routing.
For nitrogen components, the primary calibration parameters considered for upland
processes were fraction of fertilizer application to top soil layer (FRT_SURFACE) and
nitrogen percolation factor (NPERCO). Initial concentrations of nitrate in soil layers and
shallow aquifers and soil organic nitrogen were found to have no affection on simulation
since a long warming up period was used in the modeling. For instream nitrogen transform processes, the settling rates for organic fraction (RS4), transform rates of mineralization (organic nitrogen to ammonia, BC3), ammonia to nitrite (BC1), and nitrite to nitrate (BC2) were verified. Algae play an important role in instream cycles of nutrients.
The die-off and growth of algae contribute organic nutrients to and consume mineral nutrients in stream water, respectively. The algal related parameters including chlorophyllalgal ratio (AI0), mass fraction of nitrogen in algae (AI1), algal settling (RS1), death
(RHOQ) and growth (MUMAX) rates were calibrated.
For phosphorus, the primary calibration parameters considered for upland
processes were fraction of fertilizer application to top soil layer (FRT_SURFACE), phosphorus percolation factor (PPERCO), soil and runoff partition factor (PGOSKD), and
concentration in groundwater (GWSOLP). Similar to nitrogen, initial concentrations were
set as defaults. For instream phosphorus transform processes, the settling rates for organic
fraction (RS5), mineralization rate (BC4), mass fraction of phosphorus in algae (AI2),
and other algal related parameters were calibrated. Since nitrogen and phosphorus cycles
are coupled by algal processes, the changes for parameters of one of them may affect simulation results of another.
For bacteria, only bacteria wash off and die off coefficients (Table 5.7) were calibrated. Other parameters, such as the fraction of manure applied to land areas that has
active colony forming units, bacteria partition coefficient between solution and soil particulates, bacteria soil partitioning coefficient between solution in top 10 mm soil and surface runoff, bacteria percolation coefficient, and temperature adjustment factor for bacteria die-off/growth were set to their default values 0.15, 0.9, 175 m3/Mg, 10 (10 m3/Mg),
and 1.07, respectively. The wash-off fraction, die-off factor for bacteria in soil solution,
die-off factor for bacteria adsorbed to soil particles, die-off factor for bacteria on foliage,
and die-off factor for bacteria in were calibrated for both E. coli and fecal coliform. Dieoff coefficients for E. coli and fecal coliform vary in the literature. Fecal coliform is considered less persistent compared to E. coli, though its die-off coefficients were found to
be much low in some studies. A conservative estimation was made for fecal coliform for
planning purpose in which the die-off coefficients of fecal coliform were assumed to be
the same as those of E. coli.
33
Table 5.6. Nutrient calibration parameters and their final calibrated values
Model
process
Parameter
FRT_SURFACE
AI0
Both
RS1
MUMAX
RHOQ
NPERCO
AI1
RS4
Nitrogen
BC1
BC2
BC3
PPERCO
PHOSKD
Phosphorus
GWSOLP
AI2
RS5
BC4
Description
Fraction of fertilizer applied to top 10mm of
soil
Ratio of chlorophyll-a to algal biomass (gchla/mg algae)
Local algal settling rate in the reach at 20 C
(m/day)
Maximum specific algal growth rate at 20 C
(1/day)
Algal respiration rate at 20 C (1/day)
Nitrate percolation coefficient (concentration of nitrate in the runoff to the concentration of nitrate in percolate)
Fraction of algal biomass that is nitrogen
(mg N/mg alg)
Rate coefficient for organic N settling in the
reach at 20 C (1/day)
Rate constant for biological oxidation of
NH4 to NO2 in the reach at 20 C in wellaerated conditions (1/day)
Rate constant for biological oxidation of
NO2 to NO3 in the reach at 20 C in wellaerated conditions (1/day)
Rate constant for hydrolysis of organic N to
NH4 in the reach at 20 C (1/day).
Phosphorus percolation coefficient (10
m3/Mg). (ratio of the solution phosphorus
concentration in the surface 10 mm of soil to
the concentration of phosphorus in percolate)
Phosphorus soil partitioning coefficient
(m3/Mg) (ratio of the soluble phosphorus
concentration in the surface 10 mm of soil to
the concentration of soluble phosphorus in
surface runoff)
Concentration of soluble phosphorus in
groundwater contribution to stream flow
from subbasin (mg P/L or ppm)
Fraction of algal biomass that is phosphorus
(mg P/mg alg)
Organic phosphorus settling rate in the reach
at 20 C (1/day)
Rate constant for mineralization of organic P
to dissolved P in the reach at 20 C (1/day)
34
Model
range
Value
used
01
0.2
10 - 100
100
0.15-1.82
1.0 3.0
0.006
0.05 - 0.5
0.0031
01
0.2
0.02 0.09
0.08
0.001 0.1
0.001
0.1 1
0.2 2
0.2-0.4
0.21
10 17.5
10
100 200
100
0.02 - 0.06
0.02
0.01 0.02
0.015
0.001 0.1
0.001
0.01 0.7
0.01
Table 5.7. Bacterial calibration parameters and their final calibrated values
Model
process
Parameter
Description
WOF_P
WDPQ
Wash-off fraction for persistent bacteria

Die-off factor for persistent bacteria in soil solution at 20C (1/day)
WDPS
Die-off factor for persistent bacteria adsorbed to
soil particles at 20C. (1/day)
E. Coli
WDPF
Die-off factor for persistent bacteria on foliage at
20C (1/day)
WDPRCH Die-off factor for persistent bacteria in streams
(moving water) at 20C. (1/day)
WOF_LP Wash-off fraction for persistent bacteria
WDLPQ Die-off factor for persistent bacteria in soil solution at 20C (1/day)
WDLPS Die-off factor for persistent bacteria adsorbed to
Fecal
soil particles at 20C. (1/day)
coliform
WDLPF Die-off factor for persistent bacteria on foliage at
20C (1/day)
WDLPRCH Die-off factor for persistent bacteria in streams
(moving water) at 20C. (1/day)
Value
used
0.25
0.1
0.01
0.2
0.4
0.25
0.1
0.01
0.2
0.4
5.5.3. Crop Yield Calibration
Crop yields were calibrated for corn, soybean and hay by comparing annual average
yields cross the whole watershed to Hunterdon County average values. For other crops,
yields were not calibrated since county statistic data were not available. Radiation use
efficiency coefficients or bio-energy ratios, harvest indexes under optimum growing and
highly stressed conditions were selected as the parameters for calibration. For soybean,
radiation use efficiency was increased 20% from the default value to 30 (kg/ha)/(MJ/m2),
and the harvest index under stressed growing conditions was set to be 0.31, the same as
under optimum conditions. Other parameters were set at their default values.
35
6. Calibration Results and Discussion

6.1. Flow Calibration
Relative sensitivity values were found in the parameter sensitivity analysis. Of the twenty
six parameters top 10 ranked sensitive parameters affecting stream flow at Reaville were
identified with the relative sensitivity values ranges from 0.008 to 0.092, which were, in
the order from high to low: channel effective hydraulic conductivity, initial SCS Curve
Number II value, base flow alpha factor, Mannings n value for main channel, surface
runoff lag, snow pack temperature lag factor, shallow aquifer for return flow to occur,
soil evaporation compensation factor, maximum plant leaf area index, and maximum canopy storage. In addition to the top 10 sensitive parameters, available water capacity of
the soil layer, groundwater revap coefficient, groundwater delay, and deep aquifer percolation coefficient were considered for model calibration according to literature. Note that,
only those parameters whose default values were adjusted during the calibration are listed
in Table 5.5.
Measured and simulated annual flows at Reaville match well (Figure 6.1 and Table
6.1). The simulated annual flows are slightly lower for the years 1997 to 1999 and
slightly higher for the years 2001 and 2002. Monthly simulated and observed stream
flows match well except for a few months, where the model underpredicts the flow September 1999 and overpredicts for June 2001 (Figure 6.2). The time series of measured
and simulated daily flows during the calibration period (Figure 6.3) show that simulated
flows are usually underpredicted on days with daily rainfall more than 15 m3/s. Over estimation occurs on days with lower daily rainfall during the summers. As aforementioned, the streamflow calibration was carried out after acceptable calibration of filtered
surface runoff and base flow. Figure 6.4 shows the graphic comparison between the filtered monthly base flows of observed and simulated stream flows at Reaville.
Means, standard deviations, R2, and NSE values indicate the good agreement between simulated and observed values for the monthly calibration at Reaville, with coefficients of determination 0.73, 0.66 and 0.72, and Nash-Sutcliffe efficiency 0.67, 0.65 and
0.69 for monthly surface runoff, base flow and total stream flow, respectively (Table 6.1).
Annual simulated and observed flows show lower fitness than at the monthly levels, due
to the limited number of years for statistics. Notable improvement in the correlation and
simulation efficiency of daily calibration of surface runoff and stream flow was found by
just switching observed streamflow values on two days, September 16 and 17 in 1999.
After the switch, coefficients of determination for daily calibration of surface runoff, base
flow and total stream flow reaches 0.66, 0.41 and 0.63, while Nash-Sutcliffe efficiency
coefficients reach 0.58, 0.37 and 0.57, respectively. The rationality of this switch is confirmed by checking the daily time series of precipitation, and simulated and observed
stream flows. As shown in Figure 6.5, there is a large rainstorm event, actually the Hurricane Floyd, arrived this watershed on September 17 in 1999 according to records at the
nearest meteorological station in Flemington. The observed high flow was recorded on
September 16, contradicting to the order of rainfall events. Actually in the original data
file, it is commented that the stream values during the Hurricane were estimated rather
36
than truly measured. The example indicates that the one-to-one match of time series of
simulated and observed values determines the coefficients of determination and NashSutcliffe efficiency, and large storm events have greater affection. It is acceptable that
calibration at the daily level has lower performance than at monthly level due to mismatch in some days. Overall, the model underpredicts flows during large storm events,
resulting about 4% to 7% lower for the mean runoff, base flow and stream flow (Table
6.1).
Table 6.2 lists various performance statistics of simulated and observed daily surface runoffs, base flows and stream flows at Reaville for each year. The NSE and R2
values are good for most of the years. However, the evaluation statistics for surface runoff and stream flow show lower NSE values for the years 2001, 2002, 2004 and 2008.
This might be caused by input (precipitation, temperature and other climate data) or
measured streamflow data uncertainty during those years. Moreover, NSE is more sensitive to extreme values hence lower NSE values can be the result of higher variability between the simulated and observed peak flows. As shown in the table, a switch of the observed stream flow on September 16 and 17 in 1999 will greatly improve NSE values
from -0.09 and -0.04 to 0.62 and 0.61 for runoff and stream flow, respectively. The
switch also improves R2 between the simulated and observed base flows but decreases
the NSE.
2.0
Simulated
Annual Flow (m3/s)
Observed
1.5
1.0
0.5
0.0
1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008
Year
Figure 6.1. Annual observed and simulated stream flows at Reaville

9
Observed
Monthly Flow (m3/s)
Simulated
5
4
3
2
1
Jan-97
Apr-97
Jul-97
Oct-97
Jan-98
Apr-98
Jul-98
Oct-98
Jan-99
Apr-99
Jul-99
Oct-99
Jan-00
Apr-00
Jul-00
Oct-00
Jan-01
Apr-01
Jul-01
Oct-01
Jan-02
Apr-02
Jul-02
Oct-02
Jan-03
Apr-03
Jul-03
Oct-03
Jan-04
Apr-04
Jul-04
Oct-04
Jan-05
Apr-05
Jul-05
Oct-05
Jan-06
Apr-06
Jul-06
Oct-06
Jan-07
Apr-07
Jul-07
Oct-07
Jan-08
Apr-08
Jul-08
Oct-08
Month
Figure 6.2. Monthly observed and simulated stream flows at Reaville
37
50
Observed
45
Simulated
40
Daily Flow (m3/s)
35
30
25
20
15
10
5
12/24/02
10/26/02
08/28/02
06/30/02
05/02/02
03/04/02
01/04/02
11/06/01
09/08/01
07/11/01
05/13/01
03/15/01
01/15/01
11/17/00
09/19/00
07/22/00
05/24/00
03/26/00
01/27/00
11/29/99
10/01/99
08/03/99
06/05/99
04/07/99
02/07/99
12/10/98
10/12/98
08/14/98
06/16/98
04/18/98
02/18/98
12/21/97
10/23/97
08/25/97
06/27/97
04/29/97
03/01/97
01/01/97
Date
Figure 6.3. Daily observed and simulated stream flows at Reaville during calibration period
2
Baseflow (m3/s)
1.8
Observed
Simulated
1.6
1.4
1.2
1
0.8
0.6
0.4
0.2
Jan-97
Apr-97
Jul-97
Oct-97
Jan-98
Apr-98
Jul-98
Oct-98
Jan-99
Apr-99
Jul-99
Oct-99
Jan-00
Apr-00
Jul-00
Oct-00
Jan-01
Apr-01
Jul-01
Oct-01
Jan-02
Apr-02
Jul-02
Oct-02
Jan-03
Apr-03
Jul-03
Oct-03
Jan-04
Apr-04
Jul-04
Oct-04
Jan-05
Apr-05
Jul-05
Oct-05
Jan-06
Apr-06
Jul-06
Oct-06
Jan-07
Apr-07
Jul-07
Oct-07
Jan-08
Apr-08
Jul-08
Oct-08
Month
Figure 6.4. Filtered monthly base flows of observed and simulated stream flows at Reaville
Table 6.1. Calibration results for flows at Reaville from 1997 to 2002
Flow
Surface runoff
Base flow
Stream flow
Annual
Mean (m3/s)
Obs
Sim
0.532 0.496
-6.77%
STDEV (m3/s)
Obs
Sim
0.218 0.120
Monthly
0.532
0.495
-6.95%
0.889
0.542
Daily
0.530
0.495
-6.60%
4.660
2.341
Annual
0.445
0.424
-4.72%
0.045
0.066
Monthly
0.445
0.424
-4.72%
0.406
0.297
Daily
0.442
0.423
-4.30%
0.676
0.460
Annual
0.977
0.920
-5.83%
0.235
0.175
Monthly
0.977
0.920
-5.83%
1.172
0.780
Daily
0.972
0.918
-5.56%
4.684
2.535
Time period
Mean relative error
R2
NSE
0.55
0.48
0.73
0.05
(0.66*)
0.10
0.67
-0.04
(0.58*)
-1.46
0.66
0.35
(0.41*)
0.46
0.65
0.32
(0.37*)
0.38
0.72
0.08
(0.63*)
0.69
0.01
(0.57*)
* Switch the observed stream flows on September 16 and 17, 1999.
38
250
Observed
Simulated
50
Precipitation
150
150
09/17/99
200
100
250
09/17/99
300
Precipitation (mm)
Daily Flow (m3/s)
100
09/16/99
200
50
350
0
12/30/99
12/19/99
12/08/99
11/27/99
11/16/99
11/05/99
10/25/99
10/14/99
10/03/99
09/22/99
09/11/99
08/31/99
08/20/99
08/09/99
07/29/99
07/18/99
07/07/99
06/26/99
06/15/99
06/04/99
05/24/99
05/13/99
05/02/99
04/21/99
04/10/99
03/30/99
03/19/99
03/08/99
02/25/99
02/14/99
02/03/99
01/23/99
01/12/99
01/01/99
400
Date
Figure 6.5. Observed and simulated and daily stream flows and precipitation during 1999
Table 6.2. Daily flow calibration and validation at Reaville for each year
Year
1997
1998
1999
2000
2001
2002
2003
2004
2005
2006
2007
2008
Surface runoff
Base flow
Stream flow
2
2
R
NSE
R
NSE
R2
NSE
0.40
0.33
0.41
0.31
0.41
0.34
0.45
0.44
0.80
0.71
0.53
0.52
0.01
-0.09
0.14
0.00
0.03
-0.04
(0.84*) (0.62*) (0.24*) (-0.21*) (0.80*) (0.61*)
0.31
0.29
0.33
0.31
0.33
0.31
0.30
-0.01
0.48
0.47
0.38
0.07
0.40
0.07
0.64
0.62
0.44
0.19
0.48
0.48
0.52
0.50
0.49
0.48
0.28
-0.03
0.40
0.16
0.29
0.01
0.39
0.30
0.50
0.30
0.44
0.35
0.43
0.43
0.67
0.66
0.47
0.47
0.40
0.39
0.57
0.54
0.44
0.43
0.19
0.10
0.66
0.66
0.25
0.18
The validation results are good for stream flows at Reaville (Figure 6.6 and Table
6.3). The simulated annual flow is slightly lower for the year 2003 (Figure 6.1). Monthly
simulated and observed stream flows match well except for a few months, where the
model underpredicts the flow in March, June and December in 2003, and April in 2007,
and overpredicts for July 2004 and November 2007 (Figure 6.2). The time series of
measured and simulated daily flows during the validation period (Figure 6.6) show that
simulated flows are usually underpredicted on days with daily rainfall more than 15 m3/s.
Means, standard deviations, R2, and NSE values indicate good agreement between
simulated and observed values for the monthly calibration at Reaville, with coefficients
of determination 0.65, 0.72 and 0.69, and Nash-Sutcliffe efficiency 0.64, 0.71 and 0.68
39
for monthly surface runoff, base flow and total stream flow, respectively (Table 6.3). Annual simulated and observed flows show higher coefficients of determination but lower
Nash-Sutcliffe efficiency than at the monthly level. Coefficients of determination for daily calibration of surface runoff, base flow and stream flow are 0.36, 0.53 and 0.39, while
Nash-Sutcliffe efficiency coefficients are 0.33, 0.44 and 0.37, respectively. The runoff
shows lower coefficients of determination and Nash-Sutcliffe efficiency compared to
base flow, however, it is acceptable for calibration at the daily level. Overall, the model
underpredicts surface runoff about 10% and overpredicts base flow about 6% during the
validation time period 2003 to 2008, and thus leads to a 3% underprediction for stream
flow.
Figure 6.7 displays the observed versus simulated stream flow duration curves at
Reaville during 1997 2008, which confirms a good agreement between observed and
simulated daily flows, however, the model generally overpredicts during days with a low
flow less than 0.1 m3/s.
50
Observed
45
Simulated
40
Daily Flow (m3/s)
35
30
25
20
15
10
5
12/23/08
8/27/08
10/25/08
5/1/08
6/29/08
3/3/08
1/4/08
9/8/07
11/6/07
7/11/07
5/13/07
3/15/07
1/15/07
11/17/06
09/19/06
07/22/06
05/24/06
03/26/06
01/26/06
11/28/05
09/30/05
08/02/05
06/04/05
04/06/05
02/06/05
12/09/04
10/11/04
08/13/04
06/15/04
04/17/04
02/18/04
12/21/03
10/23/03
08/25/03
06/27/03
04/29/03
03/01/03
01/01/03
Date
Figure 6.6. Daily observed and simulated stream flows at Reaville during validation period
Table 6.3. Validation results for flows at Reaville from 2003 to 2008
Flow
Time period
Surface runoff
Base flow
Stream flow
Annual
Monthly
Daily
Annual
Monthly
Daily
Annual
Monthly
Daily
Mean (m3/s)
Obs
Sim
0.766 0.688
0.766 0.688
0.764 0.686
0.619 0.654
0.619 0.654
0.618 0.653
1.385 1.341
1.385 1.341
1.382 1.339
Mean relative error

-10.18%
-10.18%
-10.21%
5.65%
5.65%
5.66%
-3.18%
-3.18%
-3.11%
STDEV (m3/s)
Obs
Sim
0.126 0.048
0.828 0.633
3.303 2.536
0.120 0.062
0.471 0.375
0.662 0.590
0.216 0.096
1.230 0.914
3.589 2.788
40
R2
NSE
0.86
0.65
0.36
0.86
0.72
0.53
0.84
0.69
0.39
-0.18
0.64
0.33
0.59
0.71
0.44
0.51
0.68
0.37
1000.000
Observed
Simulated
30%
50%
Daily flow (m3/s)
100.000
10.000
1.000
0.100
0.010
0.001
0.000
0%
10%
20%
40%
60%
70%
80%
90%
100%
Percent of time that flow is equaled or exceeded
Figure 6.7. Observed versus simulated stream flow duration curves at Reaville, 1997 to 2008
6.2. Sediment Calibration
Observations show that high TSS concentrations and loads at Reaville are usually happened with occurrence of high stream flows when high precipitation generates more runoff and soil erosion (Figure 6.8). The simulated daily flows with calibrated SWAT model generally have good consistence with observed daily flows, except for some days with
high rainfall events. The USGS observed instantaneous flows from water quality sampling during 1991 to 2008 are close to corresponding daily flows in most times, but are
more than double of daily flows on 7/13/1996 and 3/19/1998 (Figure 6.9). The sediment
calibration was carried out such that simulated TSS concentrations matched observed instantaneous concentrations as far as possible.
There are two days having extremely high observed instantaneous TSS concentrations, which are 205 and 302 mg/L on 07/24/1997 and 03/19/98, respectively. The simulated daily TSS concentrations are much lower, at 39.728 and 26.305 mg/L on those two
days, respectively. Also on 07/24/1997 and 03/19/98, the observed TSS loads are 75 and
759 Mg/d, which are significantly larger than simulated loads of 41.190 and 8.500 Mg/d,
respectively. In other sampling days, observed and simulated loads are comparable. A
visual comparison with the concentration (Figure 6.10) and loading (Figure 6.11) graphs,
in which the observed TSS values on those two days are excluded, indicates a good approximate sediment calibration.
Table 6.4 gives out the statistic results of TSS loading calibration and validation at
Reaville. Average simulated loads and standard deviation for sediment are much lower
than observed values if the two extreme observed loads are included. Once the two extreme values are excluded, the mean observed and simulated loads during calibration period are 2.388 Mg/d and 2.236 Mg/d, and standard deviations are 5.287 Mg/d and 5.372
Mg/d, respectively. The slight underprediction of sediment loads by the model is mainly
due to the underprediction of stream flows during high rain fall events. Given the facts
41
8/13/1991
10/29/1991
2/6/1992
3/18/1992
5/27/1992
7/23/1992
11/5/1992
2/17/1993
4/6/1993
6/9/1993
7/26/1993
11/23/1993
2/1/1994
3/23/1994
5/25/1994
8/31/1994
5/2/1996
5/21/1996
6/4/1996
6/18/1996
7/10/1996
7/13/1996
8/7/1996
9/3/1996
10/8/1996
11/13/1996
12/10/1996
1/6/1997
2/25/1997
4/1/1997
4/24/1997
5/19/1997
6/12/1997
7/24/1997
8/21/1997
10/8/1997
11/18/1997
12/23/1997
1/16/1998
2/23/1998
3/19/1998
4/9/1998
5/7/1998
6/10/1998
6/1/2000
8/30/2000
2/10/2005
6/1/2005
6/6/2006
11/14/2007
4/29/2008
08/13/91
10/29/91
02/06/92
03/18/92
05/27/92
07/23/92
11/05/92
02/17/93
04/06/93
06/09/93
07/26/93
11/23/93
02/01/94
03/23/94
05/25/94
08/31/94
05/02/96
05/21/96
06/04/96
06/18/96
07/10/96
07/13/96
08/07/96
09/03/96
10/08/96
11/13/96
12/10/96
01/06/97
02/25/97
04/01/97
04/24/97
05/19/97
06/12/97
07/24/97
08/21/97
10/08/97
11/18/97
12/23/97
01/16/98
02/23/98
03/19/98
04/09/98
05/07/98
06/10/98
06/01/00
08/30/00
02/10/05
06/01/05
06/06/06
11/14/07
04/29/08
08/13/91
10/29/91
02/06/92
03/18/92
05/27/92
07/23/92
11/05/92
02/17/93
04/06/93
06/09/93
07/26/93
11/23/93
02/01/94
03/23/94
05/25/94
08/31/94
05/02/96
05/21/96
06/04/96
06/18/96
07/10/96
07/13/96
08/07/96
09/03/96
10/08/96
11/13/96
12/10/96
01/06/97
02/25/97
04/01/97
04/24/97
05/19/97
06/12/97
07/24/97
08/21/97
10/08/97
11/18/97
12/23/97
01/16/98
02/23/98
03/19/98
04/09/98
05/07/98
06/10/98
06/01/00
08/30/00
02/10/05
06/01/05
06/06/06
11/14/07
04/29/08
that there were only a few sampling days per year to calibrate the model, and matching
the daily simulated values to those days alone is tedious, the results obtained seem to be
reasonable. Note that the observed TSS loads are computed from the product of instantaneous stream flows and concentrations of samples, while the simulated loads are daily
outputs, hence they are not the same items and the comparison is just used for approximate calibration.
45
40
35
30
25
20
15
10
5
0
Observed instantaneous flow (m3/s)
600
Observed instantaneous TSS concentration (mg/L)
500
400
300
200
100
200
Observed instantaneous load (Mg/d)
160
120
2020
42
759
80
40
Figure 6.8. Observed instantaneous stream flows, TSS concentrations and loads based on
water quality sampling at Reaville
40
Obserbed instanteneous flow
35
Observed daily flow
30
Simulated daily flow
Flow (m3/s)
45
25
20
15
10
5
8/28/2008
11/28/06
11/14/200
07/19/06
11/16/05
07/13/05
08/09/04
07/07/04
05/13/03
02/28/02
11/21/00
08/19/99
06/10/98
02/23/98
11/18/97
09/22/97
05/22/97
02/25/97
11/13/96
07/16/96
05/23/96
01/23/96
02/02/95
02/01/94
02/17/93
02/06/92
02/13/91
Figure 6.9. Observed instantaneous and daily flows loads and SWAT simulated daily flows
at Reaville on water quality sampling days
80
Observed
70
Simulated
TSS (mg/L)
60
50
40
30
20
10
6/4/2002
12/6/2001
6/9/2001
12/11/2000
6/14/2000
12/17/1999
6/20/1999
12/22/1998
6/25/1998
12/27/1997
6/30/1997
1/1/1997
Figure 6.10. Simulated and USGS measured TSS concentrations at Reaville during the calibration period
100
Observed
90
Simulated
TSS (Mg/d)
80
70
60
50
40
30
20
10
6/4/2002
12/6/2001
6/9/2001
12/11/2000
6/14/2000
12/17/1999
6/20/1999
12/22/1998
6/25/1998
12/27/1997
6/30/1997
1/1/1997
Figure 6.11. Simulated and USGS measured TSS loads at Reaville during the calibration
period
43
Table 6.4. Statistics of TSS loading calibration and validation at Reaville

Period
Obs (Mg/d)
Sim (Mg/d)
1997-2002 mean (19 days)

1997-2002 STDEV
2003-2008 mean (5 days)
46.031 (2.388*)
173.524(5.287*)
3.474
5.011 (2.236*)
11.631 (5.372*)
3.505
2003-2008 STDEV
6.484
5.388
* After the removal the two days with daily load 75 Mg/d.
Figure 6.12 and Figure 6.13 present the discrete USGS observed TSS concentrations and loads along with the simulated time series of daily average values, respectively.
An initial visual comparison constitutes a good sediment validation. The mean USGS observed and simulated loads are 3.474 Mg/d and 3.505 Mg/d, and their standard deviations
are 6.484 Mg/d and 5.388 Mg/d, respectively. The statistics show good agreement between the simulated and observed loads although this is based on limited number of sampling days. Good agreements were also obtained with the addition water quality monitoring data at the seven designed sites through the Neshanic River watershed restoration
plan project. Plots comparing simulated time series of TSS concentration with observed
data obtained during the project at seven sites are presented in Figure 6.14 to Figure 6.20.
Note that many of the sampling days were low flow days which cause corresponding low
observed and simulated loads.
80
Observed
70
Simulated
TSS (mg/L)
60
50
40
30
20
10
10/5/2008
4/8/2008
10/11/2007
4/14/2007
10/16/2006
4/19/2006
10/21/2005
4/24/2005
10/26/2004
4/29/2004
11/1/2003
5/5/2003
11/6/2002
Figure 6.12. Simulated and USGS measured TSS concentrations at Reaville during the validation period
44
45
Dec-08
Nov-08
Oct-08
Sep-08
Aug-08
Jul-08
Jun-08
Dec-08
Nov-08
Oct-08
Sep-08
Aug-08
Jul-08
Jun-08
May-08
Apr-08
Mar-08
10/5/2008
4/8/2008
10/11/2007
4/14/2007
10/16/2006
4/19/2006
10/21/2005
Observed
May-08
Apr-08
Mar-08
Feb-08
Jan-08
Dec-07
4/24/2005
10/26/2004
4/29/2004
11/1/2003
5/5/2003
11/6/2002
TSS (Mg/d)
90
Feb-08
Jan-08
Dec-07
100
Nov-07
Oct-07
Sep-07
Aug-07
Jul-07
Jun-07
May-07
Apr-07
Mar-07
Feb-07
Jan-07
TSS (mg/L)
60
Nov-07
Oct-07
Sep-07
Aug-07
Jul-07
Jun-07
May-07
Apr-07
Mar-07
Feb-07
Jan-07
TSS (mg/L)
100
80
Simulated
70
60
50
40
30
20
10
Figure 6.13. Simulated and USGS measured TSS loads at Reaville during the validation period
70
Observed
Simulated
50
40
30
20
10
Figure 6.14. Simulated and project measured TSS concentrations at Reaville (N1)
120
Observed
Simulated
80
60
40
20
Figure 6.15. Simulated and project measured TSS concentrations at FN1
Jan-07
46
Dec-08
Nov-08
Oct-08
Sep-08
Aug-08
Jul-08
Jun-08
May-08
Apr-08
Mar-08
Feb-08
Jan-08
60
Dec-08
Nov-08
Oct-08
Sep-08
Aug-08
Jul-08
Jun-08
May-08
Apr-08
Mar-08
Feb-08
Jan-08
Dec-07
Nov-07
Oct-07
Sep-07
Aug-07
Jul-07
Jun-07
May-07
Apr-07
Mar-07
60
Dec-07
Jan-07
Feb-07
TSS (mg/L)
Jan-07
Dec-08
Nov-08
Oct-08
Sep-08
Aug-08
Jul-08
Jun-08
May-08
Apr-08
Mar-08
Feb-08
Jan-08
Dec-07
Nov-07
Oct-07
Sep-07
Aug-07
Jul-07
Jun-07
May-07
Apr-07
Mar-07
Feb-07
TSS (mg/L)
35
Nov-07
Oct-07
Sep-07
Aug-07
Jul-07
Jun-07
May-07
Apr-07
Mar-07
Feb-07
TSS (mg/L)
40
Observed
Simulated
30
25
20
15
10
Figure 6.16. Simulated and project measured TSS concentrations at SN1

70
Observed
Simulated
50
40
30
20
10
Figure 6.17. Simulated and project measured TSS concentrations at TN3
70
Observed
Simulated
50
40
30
20
10
Figure 6.18. Simulated and project measured TSS concentrations at TN3a
70
Observed
Simulated
60
TSS (mg/L)
50
40
30
20
10
Dec-08
Oct-08
Nov-08
Sep-08
Jul-08
Aug-08
Jun-08
Apr-08
May-08
Mar-08
Jan-08
Feb-08
Dec-07
Oct-07
Nov-07
Aug-07
Sep-07
Jul-07
Jun-07
May-07
Apr-07
Mar-07
Jan-07
Feb-07
Figure 6.19. Simulated and project measured TSS concentrations at UNT1

120
Observed
Simulated
TSS (mg/L)
100
80
60
40
20
Dec-08
Oct-08
Nov-08
Sep-08
Jul-08
Aug-08
Jun-08
May-08
Apr-08
Mar-08
Feb-08
Jan-08
Nov-07
Dec-07
Oct-07
Sep-07
Aug-07
Jul-07
Jun-07
May-07
Apr-07
Mar-07
Feb-07
Jan-07
Figure 6.20. Simulated and project measured TSS concentrations at UNT2
6.3. Nutrient Calibration
To obtain a reasonable calibration, the algal growth and death rates at 20 C were set outside the recommended ranges in SWAT. The best fit for instream concentrations of various forms of nitrogen and phosphorus was obtained with low algal growth and death
rates. The concentrations of organic N and P, ammonia nitrogen, and mineral P are sensitive to algal growth and death rates. A high death rate would cause unreasonable high
peaks of mineral and organic N/P concentrations, because SWAT simulates chlorophyll
in surface runoff and tributaries without accounting the transform into nutrients but calculate the transform through algal die-off process once water enters into the main reaches of
subbasins. On the contrary, a high algal growth rate would cause ammonia nitrogen and
TP concentrations lower than observed data when algal death rate was set to be low.
SWAT modeling results are presented graphically for the USGS station and the
seven project calibration sites in Figure 6.21 to Figure 6.65. The graphs compare ob47
served versus simulated daily ammonia, nitrite + nitrate (NO2+NO3) and total nitrogen
(TN), mineral (MinP) and total phosphorus (TP) concentrations. These daily time series
graphs allow visual assessment of the models ability to reproduce observed trends, although it should be noted that the model predicts daily averages, whereas the observations are point-in-time grabs. Because the observations are not daily averages, they are
likely to exhibit greater variability than model predictions.
A second type of graphs, simulated and observed load duration curves were also
plotted and compared for water quality calibration purpose. The load duration curves plot
loads and matching flow occurrence frequencies and are often applied to find TMDL
goals and target reductions. The load duration curves are presented in Section 7.1.7.
TMDL Targets.
0.6
Observed
Simulated
NH4-N (mg/L)
0.5
0.4
0.3
0.2
0.1
12/1/2002
6/4/2002
12/6/2001
6/9/2001
12/11/2000
6/14/2000
12/17/1999
6/20/1999
12/22/1998
6/25/1998
12/27/1997
6/30/1997
1/1/1997
during the calibration period
0.7
Observed
Simulated
0.6
NH4-N (mg/L)
0.5
0.4
0.3
0.2
0.1
11/30/2008
6/3/2008
12/6/2007
6/9/2007
12/11/2006
6/14/2006
12/16/2005
6/19/2005
12/21/2004
6/24/2004
12/27/2003
6/30/2003
1/1/2003
during the validation period
48
30
Observed
Simulated
NO2NO3-N (mg/L)
25
20
15
10
5
12/1/2002
6/4/2002
12/6/2001
6/9/2001
12/11/2000
6/14/2000
12/17/1999
6/20/1999
12/22/1998
6/25/1998
12/27/1997
6/30/1997
1/1/1997
Figure 6.23. Simulated and USGS measured nitrite + nitrate concentrations at Reaville during the calibration period
20
Observed
18
Simulated
NO2NO3-N (mg/L)
16
14
12
10
8
6
4
2
11/30/2008
6/3/2008
12/6/2007
6/9/2007
12/11/2006
6/14/2006
12/16/2005
6/19/2005
12/21/2004
6/24/2004
12/27/2003
6/30/2003
1/1/2003
Figure 6.24. Simulated and USGS measured nitrite + nitrate concentrations at Reaville during the validation period
30
Observed
Simulated
25
TN (mg/L)
20
15
10
5
12/1/2002
6/4/2002
12/6/2001
6/9/2001
12/11/2000
6/14/2000
12/17/1999
6/20/1999
12/22/1998
6/25/1998
12/27/1997
6/30/1997
1/1/1997
Figure 6.25. Simulated and USGS measured TN concentrations at Reaville during the calibration period
49
20
Observed
18
Simulated
16
TN (mg/L)
14
12
10
8
6
4
2
11/30/2008
6/3/2008
12/6/2007
6/9/2007
12/11/2006
6/14/2006
12/16/2005
6/19/2005
12/21/2004
6/24/2004
12/27/2003
6/30/2003
1/1/2003
Figure 6.26. Simulated and USGS measured TN concentrations at Reaville during the validation period
0.25
Observed
Simulated
MinP (mg/L)
0.2
0.15
0.1
0.05
12/1/2002
6/4/2002
12/6/2001
6/9/2001
12/11/2000
6/14/2000
12/17/1999
6/20/1999
12/22/1998
6/25/1998
12/27/1997
6/30/1997
1/1/1997
calibration period
0.2
Observed
0.18
Simulated
0.16
MinP (mg/L)
0.14
0.12
0.1
0.08
0.06
0.04
0.02
11/30/2008
6/3/2008
12/6/2007
6/9/2007
12/11/2006
6/14/2006
12/16/2005
6/19/2005
12/21/2004
6/24/2004
12/27/2003
6/30/2003
1/1/2003
validation period
50
0.8
Observed
0.7
Simulated
TP (mg/L)
0.6
0.5
0.4
0.3
0.2
0.1
12/1/2002
6/4/2002
12/6/2001
6/9/2001
12/11/2000
6/14/2000
12/17/1999
6/20/1999
12/22/1998
6/25/1998
12/27/1997
6/30/1997
1/1/1997
Figure 6.29. Simulated and USGS measured TP concentrations at Reaville during the calibration period
0.9
Observed
0.8
Simulated
0.7
TP (mg/L)
0.6
0.5
0.4
0.3
0.2
0.1
11/30/2008
6/3/2008
12/6/2007
6/9/2007
12/11/2006
6/14/2006
12/16/2005
6/19/2005
12/21/2004
6/24/2004
12/27/2003
6/30/2003
1/1/2003
Figure 6.30. Simulated and USGS measured TP concentrations at Reaville during the validation period
51
Jan-07
52
Dec-08
Nov-08
Oct-08
Sep-08
Aug-08
Jul-08
Jun-08
May-08
Apr-08
Mar-08
0.3
Dec-08
Nov-08
Oct-08
Sep-08
Aug-08
Jul-08
Jun-08
May-08
Apr-08
Mar-08
Feb-08
Jan-08
Dec-07
Nov-07
Oct-07
Sep-07
Aug-07
Jul-07
Jun-07
May-07
Apr-07
Mar-07
0.4
Feb-08
Jan-07
Feb-07
NH4-N (mg/L)
Jan-07
Dec-08
Nov-08
Oct-08
Sep-08
Aug-08
Jul-08
Jun-08
May-08
Apr-08
Mar-08
Feb-08
Jan-08
Dec-07
Nov-07
Oct-07
Sep-07
Aug-07
Jul-07
Jun-07
May-07
Apr-07
Mar-07
Feb-07
NH4-N (mg/L)
0.4
Jan-08
Dec-07
Nov-07
Oct-07
Sep-07
Aug-07
Jul-07
Jun-07
May-07
Apr-07
Mar-07
Feb-07
NH4-N (mg/L)
0.45
0.5
Observed
Simulated
0.35
0.25
0.3
0.2
0.15
0.05
0.1
Figure 6.31. Simulated and project measured ammonia nitrogen concentrations at Reaville
(N1)
0.45
Observed
Simulated
0.35
0.3
0.25
0.15
0.2
0.05
0.1
Figure 6.32. Simulated and project measured ammonia nitrogen concentrations at FN1
0.35
Observed
Simulated
0.25
0.2
0.15
0.1
0.05
Figure 6.33. Simulated and project measured ammonia nitrogen concentrations at SN1
53
Dec-08
Nov-08
Oct-08
Sep-08
Aug-08
Jul-08
Jun-08
May-08
Apr-08
Mar-08
Feb-08
0.3
Jan-08
Dec-08
Nov-08
Oct-08
Sep-08
Aug-08
Jul-08
Jun-08
May-08
Apr-08
Mar-08
Feb-08
1.2
Jan-08
Dec-07
Nov-07
Oct-07
Sep-07
Aug-07
Jul-07
Jun-07
May-07
Apr-07
Mar-07
Feb-07
Jan-07
NH4-N (mg/L)
Dec-08
Nov-08
Oct-08
Sep-08
Aug-08
Jul-08
Jun-08
May-08
Apr-08
Mar-08
Feb-08
Jan-08
Dec-07
Nov-07
Oct-07
Sep-07
Aug-07
Jul-07
Jun-07
May-07
Apr-07
Mar-07
Feb-07
Jan-07
NH4-N (mg/L)
1.2
Dec-07
Nov-07
Oct-07
Sep-07
Aug-07
Jul-07
Jun-07
May-07
Apr-07
Mar-07
Feb-07
Jan-07
NH4-N (mg/L)
1.4
Observed
Simulated
0.8
0.6
0.4
0.2
Figure 6.34. Simulated and project measured ammonia nitrogen concentrations at TN3
1.4
Observed
Simulated
0.8
0.6
0.4
0.2
Figure 6.35. Simulated and project measured ammonia nitrogen concentrations at TN3a
0.35
Observed
Simulated
0.25
0.2
0.15
0.1
0.05
Jan-07
54
Dec-08
Nov-08
Oct-08
Sep-08
Aug-08
Jul-08
Jun-08
May-08
Apr-08
Mar-08
Feb-08
6
Dec-08
Nov-08
Oct-08
Sep-08
Aug-08
Jul-08
Jun-08
May-08
Apr-08
Mar-08
Feb-08
Jan-08
Dec-07
Nov-07
Oct-07
Sep-07
Aug-07
Jul-07
Jun-07
May-07
Apr-07
Mar-07
Jan-07
Dec-08
Nov-08
Oct-08
Sep-08
Aug-08
Jul-08
Jun-08
May-08
Apr-08
Mar-08
Feb-08
Jan-08
Dec-07
Nov-07
Oct-07
Sep-07
Aug-07
Jul-07
Jun-07
May-07
Apr-07
Mar-07
Feb-07
NH4-N (mg/L)
0.4
Jan-08
Jan-07
Feb-07
NO2NO3-N (mg/L)
12
Dec-07
Nov-07
Oct-07
Sep-07
Aug-07
Jul-07
Jun-07
May-07
Apr-07
Mar-07
Feb-07
NO2NO3-N (mg/L)
0.45
0.5
Observed
Simulated
0.35
0.25
0.3
0.2
0.15
0.05
0.1
14
Observed
Simulated
10
Figure 6.38. Simulated and project measured nitrite +nitrate concentrations at Reaville
(N1)
Observed
Simulated
Figure 6.39. Simulated and project measured nitrite +nitrate concentrations at FN1
Jan-07
55
Dec-08
Nov-08
Oct-08
Sep-08
Aug-08
Jul-08
Jun-08
May-08
Apr-08
Mar-08
Feb-08
Jan-08
25
Dec-08
Nov-08
Oct-08
Sep-08
Aug-08
Jul-08
Jun-08
May-08
Apr-08
Mar-08
Feb-08
Jan-08
Dec-07
Nov-07
Oct-07
Sep-07
Aug-07
Jul-07
Jun-07
May-07
Apr-07
Mar-07
Dec-08
Nov-08
Oct-08
Sep-08
Aug-08
Jul-08
Jun-08
May-08
Apr-08
Mar-08
Feb-08
Jan-08
Dec-07
Nov-07
Oct-07
Sep-07
Aug-07
Jul-07
Jun-07
May-07
Apr-07
Mar-07
Feb-07
Jan-07
NO2NO3-N (mg/L)
4
Dec-07
Jan-07
Feb-07
NO2NO3-N (mg/L)
25
Nov-07
Oct-07
Sep-07
Aug-07
Jul-07
Jun-07
May-07
Apr-07
Mar-07
Feb-07
NO2NO3-N (mg/L)
4.5
5
Observed
Simulated
3.5
2.5
1.5
0.5
1
Figure 6.40. Simulated and project measured nitrite +nitrate concentrations at SN1
30
Observed
Simulated
20
15
10
Figure 6.41. Simulated and project measured nitrite +nitrate concentrations at TN3
30
Observed
Simulated
20
15
10
Figure 6.42. Simulated and project measured nitrite +nitrate concentrations at TN3a
56
Dec-08
Nov-08
Oct-08
Sep-08
Aug-08
Jul-08
Jun-08
May-08
Apr-08
Mar-08
12
Jan-08
Dec-08
Nov-08
Oct-08
Sep-08
Aug-08
Jul-08
Jun-08
May-08
Apr-08
Mar-08
Feb-08
Jan-08
Feb-08
4.5
Dec-07
Nov-07
Oct-07
Sep-07
Aug-07
Jul-07
Jun-07
May-07
Apr-07
Mar-07
Feb-07
Jan-07
NO2NO3-N (mg/L)
Jan-07
Dec-08
Nov-08
Oct-08
Sep-08
Aug-08
Jul-08
Jun-08
May-08
Apr-08
Mar-08
Feb-08
Jan-08
Dec-07
Nov-07
Oct-07
Sep-07
Aug-07
Jul-07
Jun-07
May-07
Apr-07
Mar-07
Feb-07
NO2NO3-N (mg/L)
5
Dec-07
Nov-07
Oct-07
Sep-07
Aug-07
Jul-07
Jun-07
May-07
Apr-07
Mar-07
Feb-07
Jan-07
TN (mg/L)
6
Observed
Simulated
Figure 6.43. Simulated and project measured nitrite +nitrate concentrations at UNT1
5
Observed
Simulated
3.5
2.5
3
1.5
2
0.5
1
Figure 6.44. Simulated and project measured nitrite +nitrate concentrations at UNT2
14
Observed
Simulated
10
Figure 6.45. Simulated and project measured TN concentrations at Reaville (N1)
57
Jan-08
Dec-08
Nov-08
Oct-08
Sep-08
Aug-08
Jul-08
Jun-08
May-08
Apr-08
Mar-08
25
Dec-08
Nov-08
Oct-08
Sep-08
Aug-08
Jul-08
Jun-08
May-08
Apr-08
Mar-08
Feb-08
Jan-08
Dec-07
Nov-07
Oct-07
Sep-07
Aug-07
Jul-07
Jun-07
May-07
Apr-07
Mar-07
Feb-08
Jan-07
Feb-07
TN (mg/L)
Jan-07
Dec-08
Nov-08
Oct-08
Sep-08
Aug-08
Jul-08
Jun-08
May-08
Apr-08
Mar-08
Feb-08
Jan-08
Dec-07
Nov-07
Oct-07
Sep-07
Aug-07
Jul-07
Jun-07
May-07
Apr-07
Mar-07
Feb-07
TN (mg/L)
7
Dec-07
Nov-07
Oct-07
Sep-07
Aug-07
Jul-07
Jun-07
May-07
Apr-07
Mar-07
Feb-07
Jan-07
TN (mg/L)
8
Observed
Simulated
Figure 6.46. Simulated and project measured TN concentrations at FN1

6
Observed
Simulated
Figure 6.47. Simulated and project measured TN concentrations at SN1
30
Observed
Simulated
20
15
10
Figure 6.48. Simulated and project measured TN concentrations at TN3
Jan-07
58
Dec-08
Nov-08
Oct-08
Sep-08
Aug-08
Jul-08
Jun-08
May-08
Apr-08
Mar-08
Feb-08
7
Dec-08
Nov-08
Oct-08
Sep-08
Aug-08
Jul-08
Jun-08
May-08
Apr-08
Mar-08
Feb-08
Jan-08
Dec-07
Nov-07
Oct-07
Sep-07
Aug-07
Jul-07
Jun-07
May-07
Apr-07
Mar-07
10
Jan-08
Jan-07
Feb-07
TN (mg/L)
Jan-07
Dec-08
Nov-08
Oct-08
Sep-08
Aug-08
Jul-08
Jun-08
May-08
Apr-08
Mar-08
Feb-08
Jan-08
Dec-07
Nov-07
Oct-07
Sep-07
Aug-07
Jul-07
Jun-07
May-07
Apr-07
Mar-07
Feb-07
TN (mg/L)
25
Dec-07
Nov-07
Oct-07
Sep-07
Aug-07
Jul-07
Jun-07
May-07
Apr-07
Mar-07
Feb-07
TN (mg/L)
30
Observed
Simulated
20
15
10
Figure 6.49. Simulated and project measured TN concentrations at TN3a

12
Observed
Simulated
Figure 6.50. Simulated and project measured TN concentrations at UNT1
Observed
Simulated
Figure 6.51. Simulated and project measured TN concentrations at UNT2
Jan-07
59
Dec-08
Nov-08
Oct-08
Sep-08
Aug-08
Jul-08
Jun-08
May-08
Apr-08
Mar-08
0.16
Dec-08
Nov-08
Oct-08
Sep-08
Aug-08
Jul-08
Jun-08
May-08
Apr-08
Mar-08
Feb-08
Jan-08
Dec-07
Nov-07
Oct-07
Sep-07
Aug-07
Jul-07
Jun-07
May-07
Apr-07
Mar-07
0.25
Feb-08
Jan-07
Feb-07
MinP (mg/L)
Jan-07
Dec-08
Nov-08
Oct-08
Sep-08
Aug-08
Jul-08
Jun-08
May-08
Apr-08
Mar-08
Feb-08
Jan-08
Dec-07
Nov-07
Oct-07
Sep-07
Aug-07
Jul-07
Jun-07
May-07
Apr-07
Mar-07
Feb-07
MinP (mg/L)
0.16
Jan-08
Dec-07
Nov-07
Oct-07
Sep-07
Aug-07
Jul-07
Jun-07
May-07
Apr-07
Mar-07
Feb-07
MinP (mg/L)
0.18
0.2
Observed
Simulated
0.14
0.12
0.08
0.1
0.06
0.04
0.02
Figure 6.52. Simulated and project measured MinP concentrations at Reaville (N1)
0.3
Observed
Simulated
0.2
0.15
0.1
0.05
Figure 6.53. Simulated and project measured MinP concentrations at FN1
0.18
Observed
Simulated
0.14
0.12
0.1
0.08
0.06
0.04
0.02
Figure 6.54. Simulated and project measured MinP concentrations at SN1
Jan-07
60
Dec-08
Nov-08
Oct-08
Sep-08
Aug-08
Jul-08
Jun-08
May-08
Apr-08
Mar-08
0.25
Dec-08
Nov-08
Oct-08
Sep-08
Aug-08
Jul-08
Jun-08
May-08
Apr-08
Mar-08
Feb-08
Jan-08
Dec-07
Nov-07
Oct-07
Sep-07
Aug-07
Jul-07
Jun-07
May-07
Apr-07
Mar-07
0.25
Feb-08
Jan-07
Feb-07
MinP (mg/L)
Jan-07
Dec-08
Nov-08
Oct-08
Sep-08
Aug-08
Jul-08
Jun-08
May-08
Apr-08
Mar-08
Feb-08
Jan-08
Dec-07
Nov-07
Oct-07
Sep-07
Aug-07
Jul-07
Jun-07
May-07
Apr-07
Mar-07
Feb-07
MinP (mg/L)
0.2
Jan-08
Dec-07
Nov-07
Oct-07
Sep-07
Aug-07
Jul-07
Jun-07
May-07
Apr-07
Mar-07
Feb-07
MinP (mg/L)
0.25
Observed
Simulated
0.15
0.1
0.05
Figure 6.55. Simulated and project measured MinP concentrations at TN3

0.3
Observed
Simulated
0.2
0.15
0.1
0.05
Figure 6.56. Simulated and project measured MinP concentrations at TN3a
0.3
Observed
Simulated
0.2
0.15
0.1
0.05
Figure 6.57. Simulated and project measured MinP concentrations at UNT1
61
Dec-08
Nov-08
Oct-08
Sep-08
Aug-08
Jul-08
Jun-08
May-08
Apr-08
Mar-08
Feb-08
1
Dec-08
Nov-08
Oct-08
Sep-08
Aug-08
Jul-08
Jun-08
May-08
Apr-08
Mar-08
Feb-08
Jan-08
Dec-07
Jan-07
Dec-08
Nov-08
Oct-08
Sep-08
Aug-08
Jul-08
Jun-08
May-08
Apr-08
Mar-08
Feb-08
Jan-08
Dec-07
Nov-07
Oct-07
Sep-07
Aug-07
Jul-07
Jun-07
May-07
Apr-07
Mar-07
Feb-07
MinP (mg/L)
0.16
Jan-08
Nov-07
Oct-07
Sep-07
Aug-07
Jul-07
Jun-07
May-07
Apr-07
Mar-07
Feb-07
Jan-07
TP (mg/L)
0.8
Dec-07
Nov-07
Oct-07
Sep-07
Aug-07
Jul-07
Jun-07
May-07
Apr-07
Mar-07
Feb-07
Jan-07
TP (mg/L)
0.18
Observed
Simulated
0.14
0.12
0.1
0.08
0.06
0.04
0.02
Figure 6.58. Simulated and project measured MinP concentrations at UNT2
0.9
Observed
Simulated
0.7
0.6
0.5
0.4
0.3
0.2
0.1
Figure 6.59. Simulated and project measured TP concentrations at Reaville (N1)
1.2
Observed
Simulated
0.8
0.6
0.4
0.2
Figure 6.60. Simulated and project measured TP concentrations at FN1
62
Dec-08
Nov-08
Oct-08
Sep-08
Aug-08
Jul-08
Jun-08
May-08
Apr-08
Mar-08
Feb-08
1.2
Dec-08
Nov-08
Oct-08
Sep-08
Aug-08
Jul-08
Jun-08
May-08
Apr-08
Mar-08
Feb-08
Jan-08
Dec-07
1.2
Jan-08
Nov-07
Oct-07
Sep-07
Aug-07
Jul-07
Jun-07
May-07
Apr-07
Mar-07
Feb-07
Jan-07
TP (mg/L)
Dec-08
Nov-08
Oct-08
Sep-08
Aug-08
Jul-08
Jun-08
May-08
Apr-08
Mar-08
Feb-08
Jan-08
Dec-07
Nov-07
Oct-07
Sep-07
Aug-07
Jul-07
Jun-07
May-07
Apr-07
Mar-07
Feb-07
Jan-07
TP (mg/L)
0.6
Dec-07
Nov-07
Oct-07
Sep-07
Aug-07
Jul-07
Jun-07
May-07
Apr-07
Mar-07
Feb-07
Jan-07
TP (mg/L)
0.7
Observed
Simulated
0.5
0.4
0.3
0.2
0.1
Figure 6.61. Simulated and project measured TP concentrations at SN1

1.4
Observed
Simulated
0.8
0.6
0.4
0.2
Figure 6.62. Simulated and project measured TP concentrations at TN3
1.4
Observed
Simulated
0.8
0.6
0.4
0.2
Figure 6.63. Simulated and project measured TP concentrations at TN3a
2
Observed
Simulated
1.8
1.6
TP (mg/L)
1.4
1.2
1
0.8
0.6
0.4
0.2
Dec-08
Oct-08
Nov-08
Sep-08
Jul-08
Aug-08
Jun-08
Apr-08
May-08
Mar-08
Feb-08
Jan-08
Dec-07
Oct-07
Nov-07
Sep-07
Jul-07
Aug-07
Jun-07
Apr-07
May-07
Mar-07
Feb-07
Jan-07
Figure 6.64. Simulated and project measured TP concentrations at UNT1

1.6
Observed
Simulated
1.4
TP (mg/L)
1.2
1
0.8
0.6
0.4
0.2
Dec-08
Oct-08
Nov-08
Sep-08
Aug-08
Jul-08
Jun-08
May-08
Apr-08
Mar-08
Feb-08
Jan-08
Dec-07
Oct-07
Nov-07
Sep-07
Jul-07
Aug-07
Jun-07
May-07
Apr-07
Mar-07
Feb-07
Jan-07
Figure 6.65. Simulated and project measured TP concentrations at UNT2
6.4. Bacteria calibration
The calibration for bacteria is challenging since no enough statistic and watershed specific data and great uncertainties for sources, such as wild life distribution and densities,
bacteria contents in manures, and septic systems failing rates and amounts to reach
streams. With literature die-off rates for fecal coliform and E. coli, the calibration mainly
focused on source loads estimation. The SWAT modeling results are presented graphically for the USGS station and the seven project calibration sites in Figure 6.66 to Figure
6.83. The graphs compare observed versus simulated daily fecal coliform and E. coli
concentrations. These daily time series graphs allow visual assessment of the models
ability to reproduce observed trends, although it should be noted that the model predicts
daily averages, whereas the observations are point-in-time grabs. Because the observations are not daily averages, they are likely to exhibit greater variability than model predictions.
63
The simulated fecal coliform and E. coli daily concentrations at Reaville match
USGS measurements well. The observed and simulated concentrations generally fall in
the same ranges during both calibration and validation time periods. There are some discrepancies evident in the simulation with higher fecal coliform concentrations at Stations
N1, FN1, UTN1 and UTN2 and higher E. coli concentrations at Stations N1, FN1, SN1
UTN1 and UTN2 during 2007. Examination of the data shows that all of these high concentration anomalies are associated with very low to moderately low flow conditions.
This situation is consistent with the fact that the monitoring task during 2007 of this
project was designed to grab samples reflecting dry weather conditions.
The absence of water quality observation data hinders the ability to understand the
necessary adjustments needed to conduct a rigorous calibration of the model. Further collections of monitoring data are necessary for adequate validation of the model. Despite
these limitations, model performance in general is good across the whole suit of monitored sites. The calibrated model generally provides results approximate to values and
trends seen in the monitoring data that were available and appears acceptable for use in
sediment, nutrients, fecal coliform and E. coli load reduction planning.
100000
Fecal coliform (cfu/100 ml)
Observed
Simulated
10000
1000
100
10
12/1/2002
6/4/2002
12/6/2001
6/9/2001
12/11/2000
6/14/2000
12/17/1999
6/20/1999
12/22/1998
6/25/1998
12/27/1997
6/30/1997
1/1/1997
Figure 6.66. Simulated and USGS measured fecal coliform concentrations at Reaville during the calibration period
100000
Observed
Simulated
10000
1000
100
10
11/30/2008
6/3/2008
12/6/2007
6/9/2007
12/11/2006
6/14/2006
12/16/2005
6/19/2005
12/21/2004
6/24/2004
12/27/2003
6/30/2003
1/1/2003
Figure 6.67. Simulated and USGS measured fecal coliform concentrations at Reaville during the validation period
64
100000
Observed
Simulated
E.coli (cfu/100 ml)
10000
1000
100
10
12/1/2002
6/4/2002
12/6/2001
6/9/2001
12/11/2000
6/14/2000
12/17/1999
6/20/1999
12/22/1998
6/25/1998
12/27/1997
6/30/1997
1/1/1997
calibration period
100000
Observed
Simulated
E. coli (cfu/100 ml)
10000
1000
100
10
11/30/2008
6/3/2008
12/6/2007
6/9/2007
12/11/2006
6/14/2006
12/16/2005
6/19/2005
12/21/2004
6/24/2004
12/27/2003
6/30/2003
1/1/2003
validation period
65
Jan-07
66
Dec-08
Nov-08
Oct-08
Sep-08
Aug-08
Jul-08
Jun-08
May-08
Dec-08
Nov-08
Oct-08
Sep-08
Aug-08
Jul-08
Jun-08
May-08
Apr-08
Mar-08
Feb-08
Jan-08
Dec-07
Nov-07
Oct-07
Sep-07
Aug-07
Jul-07
Jun-07
May-07
Apr-07
Mar-07
10000
Apr-08
10000
Mar-08
Jan-07
Feb-07
Jan-07
Dec-08
Nov-08
Oct-08
Sep-08
Aug-08
Jul-08
Jun-08
May-08
Apr-08
Mar-08
Feb-08
Jan-08
Dec-07
Nov-07
Oct-07
Sep-07
Aug-07
Jul-07
Jun-07
May-07
Apr-07
Mar-07
Feb-07

10000
Feb-08
Jan-08
Dec-07
Nov-07
Oct-07
Sep-07
Aug-07
Jul-07
Jun-07
May-07
Apr-07
Mar-07
Feb-07
100000
Observed
Simulated
1000
100
10
Figure 6.70. Simulated and project measured fecal coliform concentrations at Reaville (N1)
100000
Observed
Simulated
1000
100
10
Figure 6.71. Simulated and project measured fecal coliform concentrations at FN1
100000
Observed
Simulated
1000
100
10
Figure 6.72. Simulated and project measured fecal coliform concentrations at SN1
Jan-07
67
Dec-08
Nov-08
Oct-08
Sep-08
Aug-08
Jul-08
Jun-08
May-08
10000
Apr-08
Dec-08
Nov-08
Oct-08
Sep-08
Aug-08
Jul-08
Jun-08
May-08
Apr-08
Mar-08
Feb-08
Jan-08
Dec-07
Nov-07
Oct-07
Sep-07
Aug-07
Jul-07
Jun-07
May-07
Apr-07
Mar-07
Jan-07
Dec-08
Nov-08
Oct-08
Sep-08
Aug-08
Jul-08
Jun-08
May-08
Apr-08
Mar-08
Feb-08
Jan-08
Dec-07
Nov-07
Oct-07
Sep-07
Aug-07
Jul-07
Jun-07
May-07
Apr-07
Mar-07
Feb-07

10000
Mar-08
Jan-07
Feb-07

10000
Feb-08
Jan-08
Dec-07
Nov-07
Oct-07
Sep-07
Aug-07
Jul-07
Jun-07
May-07
Apr-07
Mar-07
Feb-07
100000
Observed
Simulated
1000
100
10
Figure 6.73. Simulated and project measured fecal coliform concentrations at TN3
100000
Observed
Simulated
1000
100
10
Figure 6.74. Simulated and project measured fecal coliform concentrations at TN3a
100000
Observed
Simulated
1000
100
10
Figure 6.75. Simulated and project measured fecal coliform concentrations at UNT1
Jan-07
68
Dec-08
Nov-08
Oct-08
Sep-08
Aug-08
Jul-08
Jun-08
May-08
10000
Dec-08
Nov-08
Oct-08
Sep-08
Aug-08
Jul-08
Jun-08
May-08
Apr-08
Mar-08
Feb-08
Jan-08
Dec-07
Nov-07
Oct-07
Sep-07
Aug-07
Jul-07
Jun-07
May-07
Apr-07
Mar-07
10000
Apr-08
Jan-07
Feb-07
Jan-07
Dec-08
Nov-08
Oct-08
Sep-08
Aug-08
Jul-08
Jun-08
May-08
Apr-08
Mar-08
Feb-08
Jan-08
Dec-07
Nov-07
Oct-07
Sep-07
Aug-07
Jul-07
Jun-07
May-07
Apr-07
Mar-07
Feb-07

10000
Mar-08
Feb-08
Jan-08
Dec-07
Nov-07
Oct-07
Sep-07
Aug-07
Jul-07
Jun-07
May-07
Apr-07
Mar-07
Feb-07
100000
Observed
Simulated
1000
100
10
Figure 6.76. Simulated and project measured fecal coliform concentrations at UNT2
100000
Observed
Simulated
1000
100
10
Figure 6.77. Simulated and project measured E. coli concentrations at Reaville (N1)
100000
Observed
Simulated
1000
100
10
Figure 6.78. Simulated and project measured E. coli concentrations at FN1
Jan-07
69
Dec-08
Nov-08
Oct-08
Sep-08
Aug-08
Jul-08
Jun-08
May-08
10000
Dec-08
Nov-08
Oct-08
Sep-08
Aug-08
Jul-08
Jun-08
May-08
Apr-08
Mar-08
Feb-08
Jan-08
Dec-07
Nov-07
Oct-07
Sep-07
Aug-07
Jul-07
Jun-07
May-07
Apr-07
Mar-07
10000
Apr-08
Jan-07
Feb-07
Jan-07
Dec-08
Nov-08
Oct-08
Sep-08
Aug-08
Jul-08
Jun-08
May-08
Apr-08
Mar-08
Feb-08
Jan-08
Dec-07
Nov-07
Oct-07
Sep-07
Aug-07
Jul-07
Jun-07
May-07
Apr-07
Mar-07
Feb-07

10000
Mar-08
Feb-08
Jan-08
Dec-07
Nov-07
Oct-07
Sep-07
Aug-07
Jul-07
Jun-07
May-07
Apr-07
Mar-07
Feb-07
100000
Observed
Simulated
1000
100
10
Figure 6.79. Simulated and project measured E. coli concentrations at SN1

100000
Observed
Simulated
1000
100
10
Figure 6.80. Simulated and project measured E. coli concentrations at TN3
100000
Observed
Simulated
1000
100
10
Figure 6.81. Simulated and project measured E. coli concentrations at TN3a
100000
Observed
Simulated
10000
1000
100
10
Dec-08
Oct-08
Nov-08
Sep-08
Jul-08
Aug-08
Jun-08
Apr-08
May-08
Mar-08
Jan-08
Feb-08
Dec-07
Oct-07
Nov-07
Sep-07
Jul-07
Aug-07
Jun-07
Apr-07
May-07
Mar-07
Jan-07
Feb-07
Figure 6.82. Simulated and project measured E. coli concentrations at UNT1

100000
Observed
Simulated
10000
1000
100
10
Dec-08
Nov-08
Oct-08
Sep-08
Aug-08
Jul-08
Jun-08
May-08
Apr-08
Mar-08
Feb-08
Jan-08
Dec-07
Nov-07
Oct-07
Sep-07
Aug-07
Jul-07
Jun-07
May-07
Apr-07
Mar-07
Jan-07
Feb-07
Figure 6.83. Simulated and project measured E. coli concentrations at UNT2
6.5. Crop Yield Calibration
The simulated annual crop yields of corn and soybean generally match well with observed average yields in Hunterdon County. The simulated corn yield is relative high in
1999 when there was an extreme flooding event happened in spring. Simulated corn
yields are relative lower than observation after year 2004, which may be because more
relative lower yield lands were converted into urban lands. Note that, the land use data in
the modeling is based on 2002 GIS layer, and may not reflect the land use changes in
most recent years.
70
Crop yield (Mg/ha)
12
10
Corn obs
Soybean sim
Corn sim
Soybean obs
8
6
4
2
0
1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008
Year
Figure 6.84. Simulated and observed annual crop yields of corn and soybean.
Crop yield (Mg/ha)
12
10
8
6
4
2
Hay obs
Hay sim
0
1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008
Year
Figure 6.85. Simulated and observed annual crop yields of hay.
71
7. Baseline Results
The calibrated and validated model was utilized for hydrological and pollutant loading
analysis under the baseline scenario during the calibration and validation time period
from 1997 to 2008.
7.1. Stream flow and Water Balance
7.1.1. Watershed Streamflow Discharges
The time series of stream flows at a location are the result of a range of climate and hydrological processes, including precipitation, surface runoff, lateral flow, and groundwater recharge and discharge. Uncertainties associated with a lot of process parameters determine the variation of time series of stream flows.
Average annual streamflow discharge at the Neshanic River Watershed outlet (subbasin 16) is 1.51E+09 ft3 per year, or equivalently 21.318 inches of precipitation.
Monthly stream flows and variations at the outlet of are depicted in Figure 7.1. The
monthly precipitation varies from 3.111 to 4.883 inches, with the highest in June and
lowest in February. For comparison purpose, monthly stream flows were represented
with the same unit as precipitation, which was obtained by dividing the outflow volume
at this location with watershed area. Monthly stream flows vary from 0.876 (August) to
2.172 inches (January), occupying 24% (August) to 66% (February) of monthly precipitation. There are six months (January to April, October and December) having average
stream flows more than 2 inches, five months (May to July, September and November)
between 1 and 2 inches, and one month (August) below 1 inch. Medians of monthly
stream flows are close to averages during January to March, May, August, November and
December, and are lower 0.3 to 0.8 inches for other months. Variations measured by the
spans between the 25th and 75th percentiles are larger during April, June, July, September,
October, November and December ranging from 1.507 (April) to 2.215 (October) mm,
compared to other months from 0.394 (May) to 0.981 (March) inches. The seasonal distribution of average monthly stream flows generally follows the pattern of precipitation,
with larger variations during some monthly due to weather changes. The changes of land
covers also affect the seasonal distribution of stream flows. Increasing vegetation covers
intercept more water and decrease stream flow. For example, even the highest precipitation happens in June, better vegetation covers during June lead to stream flow lower than
those during fall, winter and spring months (September to April).
72
Precipitation
Median
25th Percentile
75th Percentile
4.5
3.5
2.5
1.5
0.5
Precipitation (in)
Flow (in)
Average
10
1
10
11
12
Month
Figure 7.1. Monthly stream flow and variation at the watershed outlet during 1997 2008
Base flow contribution to stream flow was evaluated by applying a digital filter
program (Arnold and Allen, 1999) which separates base flow portions through three
passes. Each pass produces a pair of time series of daily base flow and runoff. The actual
average base flow contribution is generally between the first and second pass averages.
Table 7.1 lists the mean fractions of base flows filtered from the observed flow at Reaville during each decades from 1930 to 2008. The variations between decades are not distinct, however there are small percentage decreases since 1970s. The actual base flow
contribution was 31%~47% in 1930s, and gradually increased to 34% ~51% in 1960s, but
fell to 30%~46% since 1970s and reached a lowest percentage of 28%~44% in 1990s,
and then back to 30%~46% in 2000s. The variations among decades may reflect the land
use change trend of converting agricultural lands into urban lands. The estimated proportion of base flow of the observed flow at Reaville is between 30%~45% during the
SWAT model calibration and validation period and it is 33%~48% for the same location
of the simulated flow. The proportion for surface runoff and base flow reveal that hydrologic processes and flow regimes in SWAT are modeled reasonably well.
Table 7.1. Base flow fractions from observed stream flow at the Reaville station
Time
period
1930-1939
1940-1949
1950-1959
1960-1969
1970-1979
1980-1989
1990-1999
2000-2008
1930-2008
1997-2008
1997-2008 (Sim)
Base flow
Fraction 1
0.47
0.48
0.49
0.51
0.46
0.46
0.44
0.46
0.47
0.45
0.48
73
Base flow
Fraction 2
0.31
0.32
0.33
0.34
0.30
0.30
0.28
0.30
0.31
0.30
0.33
Base flow
Fraction 3
0.25
0.25
0.26
0.27
0.24
0.24
0.22
0.24
0.24
0.24
0.28
7.1.2. Water Yields, Balance and Source Assessment

The main components of water balance for soil moisture include: the total amount
of precipitation falling on the lands, actual evapotranspiration from the basin, surface runoff, lateral flow contribution to stream flow (water flowing laterally within the soil profile that enters the main channel), soil water content and percolation. Water yield is the
net amount of water that leaves the basin and contributes to stream flow in the reach. The
water yield includes surface runoff contribution to stream flow, lateral flow contribution
to stream flow, groundwater contribution to stream flow (water from the shallow aquifer
that returns to the reach) minus the transmission losses (water lost from tributary channels in the HRU via transmission through the bed and becomes recharge for the shallow
aquifer).
To understand the prediction performance of SWAT2005 model for different rainfall conditions the simulated annual average rainfall and other hydrological components
for the Neshanic River Watershed over the years from 1997 to 2008 are compared and
listed in Table 7.2. The results indicate that more than 50% of the annual precipitation is
lost by evapotranspiration in the basin during dry years as compared to less than 50%
during wet years. Lateral flow contribution to stream flow and tributary loss in the watershed are not significant. Water yields mainly come from surface runoff and groundwater discharge. According to the annual precipitations, 1997 and 1998 are two dry years,
and 2003 and 2006 are two wet years during the simulation period. The use of the term
dry is relative as the rainfall is greater than 40 inches. The wet years produce larger water yields than the dry years. In wet years 2003 and 2006, surface runoff annual contributions to stream flow are 66.3% and 65.1% and groundwater contributions are 33.0% and
34.2%, while mean soil water contents are 5.5 and 5.6 inches, respectively,. In dry years
1997 and 1998, surface runoff annual contributions are 70.4% and 62.6% and groundwater contributions are 28.9% and 37.4%, while mean soil water contents are 5.6 and 4.7
inches, respectively. Therefore, surface runoff dominates water yield no matter in a wet
or dry year. Compared to wet years, the annual base flow contribution to stream flow during a dry year may be increased or reduced depending on the initial soil water content and
temporal distribution of precipitation over the year.
Average annual water yields from subwatershed lands during the simulation period
are given in Table 7.3. Annual water yields of subbasins range from 19.908 inch/yr to
24.010 inch/yr. Surface runoff is the main component of water yields, contributing
57.62% to 76.02%, while groundwater is the second main component contributing to
23.37% to 40.85%. The contributions from lateral flow are small, less than 3%. The Average annual water yield exported from watershed outlet is 21.689 inch/yr, of which
68.54%, 30.44% and 1.02% are contributed from surface runoff, groundwater and lateral
flow, respectively.
The average annual water yields of land uses and per unit area of land uses in the
whole watershed are given in Table 7.4 and Table 7.5, respectively. Residential-low density, corn, soybean, timothy, forest-deciduous, and wetlands-forested lands generate water yields more than 108 ft3/yr, as their areas are larger than 1100 acres. Other land uses
have less water yields, in the range of 7.119E+06 to 7.535E+07 ft3/yr. The water yields
from failing septic systems and cattle direct deposit are negligible compared with those
74
from uplands. Water yields per unit area of land uses are more than 30 inches per year for
residential-high density, commercial, institutional, and transportation lands. Rye, hay,
timothy, orchard, and forest-mixed lands generate water yields less than 20 inches per
year.
Average annual water yields of land uses in each subbasin during 1997- 2008 as
shown in Table 7.6 are grouped into five classifications, urban, row crop, other agriculture, forest and wetland. The urban lands include residential-high density, residentialmedium density, residential-med/low density, residential-low density, commercial, institutional and transportation uses. Row crop lands are agricultural land-generic, corn, soybean and rye. Other agriculture includes hay, timothy, pasture and orchard lands. The
grouped urban lands have larger variations ranging from 17.213 in/yr (subbasin 18) to
26.624 in/yr (subbasin 9) among subbasins due to the difference in compositions of land
uses. Lower urban water yield result from the contribution of dominant percentages of
residential-medium density, residential-med/low density and residential-low density,
since they generate less water yield per unit land area.
Table 7.2. Water balance components on an annual average basis for the Neshanic river
watershed
Rainfall
(in)
ET
(in)
SurQ
(in)
LatQ
(in)
GWQ
(in)
WYLD
(in)
SW
(in)
PERC
(in)
TLOSS
(in)
41.4
23.5
10.0
0.1
4.1
14.2
5.6
6.4
0.076
41.6
21.6
10.2
0.2
6.1
16.3
4.7
11.9
0.081
50.3
21.3
17.4
0.2
5.2
22.7
5.5
10.7
0.089
2000
45.2
25.5
10.2
0.1
4.1
14.4
5.5
7.7
0.080
2001
46.6
24.7
14.1
0.2
5.4
19.6
5.1
9.6
0.089
2002
2003
(Wet)
2004
49.6
23.3
13.1
0.2
5.5
18.7
5.7
12.3
0.089
64.3
25.0
18.9
0.3
9.4
28.5
5.5
20.2
0.119
56.1
25.3
17.0
0.2
7.7
24.9
5.7
13.4
0.102
55.2
22.0
18.1
0.2
7.5
25.7
5.7
14.8
0.103
59.9
24.7
17.5
0.3
9.2
26.9
5.6
17.6
0.107
57.0
22.6
17.5
0.2
6.8
24.4
6.0
15.8
0.109
Period
1997
(Dry)
1998
(Dry)
1999
2005
2006
(Wet)
2007
2008
51.4
21.9
15.4
0.3
8.2
23.8
5.6
14.5
0.103
ET = Actual evapotranspiration from HRU, SW = Soil water content, PERC = Water that percolates past
the root zone during the time step, SURQ = Surface runoff contribution to stream flow during time step,
TLOSS = Transmission losses, water lost from tributary channels in the HRU via transmission through the
bed, GWQ = Ground water contribution to stream flow, LATQ = Lateral flow contribution to stream flow,
WYLD = water yield (WYLD = SURQ + LATQ + GWQ TLOSS pond abstractions), SW = Change
of soil water content (SW = Rainfall ET SURQ LATQ PERC).
75
Table 7.3. Average annual water yields of subbasins during 1997- 2008
51.545
Water
yielda
(inch/yr)
21.147
Surface
runoff
(%)
67.01%
689.424
51.545
21.923
1082.322
51.545
726.490
1.89%
Groundwater
discharge
(%)
31.09%
70.44%
2.65%
26.92%
20.812
73.31%
0.64%
26.05%
51.545
24.010
76.02%
0.61%
23.37%
333.592
51.545
22.534
69.46%
0.34%
30.20%
1109.503
51.545
21.742
66.49%
0.31%
33.20%
956.298
51.545
19.908
62.01%
1.15%
36.83%
738.845
51.545
20.704
61.16%
1.28%
37.56%
434.905
51.545
23.984
75.48%
0.16%
24.36%
10
580.698
51.545
21.031
65.31%
0.65%
34.04%
11
879.695
51.545
23.581
75.30%
0.60%
24.11%
12
958.769
51.545
22.284
71.58%
0.86%
27.56%
13
555.987
51.545
20.706
59.09%
2.86%
38.05%
14
622.706
51.545
21.187
66.90%
1.43%
31.68%
15
664.713
51.545
20.916
66.60%
1.37%
32.03%
16
879.695
51.545
21.693
69.23%
0.80%
29.97%
17
652.358
51.545
22.927
73.84%
0.42%
25.73%
18
709.192
51.545
21.107
65.84%
0.62%
33.54%
19
625.177
51.545
22.554
73.56%
0.65%
25.78%
20
511.508
51.545
22.672
72.88%
0.35%
26.77%
21
995.835
51.545
19.958
57.62%
1.53%
40.85%
22
654.829
51.545
22.231
65.37%
1.58%
33.05%
23
1272.593
51.545
22.094
71.19%
0.71%
28.11%
24
775.911
51.545
21.668
70.24%
0.29%
29.47%
25
622.706
51.545
21.602
66.16%
1.68%
32.15%
Watershed
19513.912
51.545
21.689
68.54%
1.02%
30.44%
Subbasin
Area (ac)
Precipitation
(inch/yr)
1480.161
Lateral
flow (%)
a. Water yield is defined as the net amount of water that leaves the subbasin and contributes to
streamflow in the main channel (reach). The surface runoff given here is the net surface contribution
to the main channel streamflow calculated by subtracting tributary channel loss from surface runoff
generated in lands. Pond abstractions are assumed to be nil.
76
Table 7.4. Average annual yields of land uses in the Neshanic River Watershed
Land
use
Area (ac)
Water yield
(ft3/yr)
Sediment
yield (ton/yr)
TN (lb/yr)
TP
(lb/yr)
URHD
92.269
1.027E+07
11.576
1021.197
107.593
URMD
190.970
1.793E+07
6.261
1115.771
137.945
URML
336.454
2.919E+07
2.310
1193.714
245.228
URLD
4899.210
3.152E+08
11.445
9421.990
1833.523
UCOM
256.733
3.050E+07
43.282
3571.587
336.459
Institutional
UINS
451.266
4.919E+07
44.507
4362.169
466.571
Transportation
Agricultural LandGeneric
Corn
UTRN
149.051
1.976E+07
71.041
3774.507
376.716
AGRL
328.947
2.834E+07
35.593
6322.259
374.734
CORN
1834.412
1.602E+08
142.733
111135.074
2907.535
Soybean
SOYB
1847.508
1.654E+08
217.696
28408.390
1940.959
Rye
RYE
321.963
2.095E+07
1.907
1110.364
127.873
Hay
HAY
748.803
5.179E+07
10.757
5175.374
144.800
Timothy
TIMO
1671.273
1.189E+08
22.316
16710.316
382.384
Pasture
PAST
892.456
7.535E+07
69.892
5074.226
1521.275
Orchard
ORCD
99.929
7.119E+06
0.141
1002.356
19.720
Forest-Deciduous
FRSD
3047.600
2.482E+08
1.650
8420.022
222.372
Forest-Evergreen
FRSE
179.554
1.329E+07
0.023
839.891
15.186
Forest-Mixed
FRST
902.409
5.762E+07
0.094
2032.460
63.204
Wetlands-Forested
WETF
1101.952
1.015E+08
0.257
12698.042
89.178
Wetlands-Mixed
Cattle direct
deposit
Septic
WETL
139.718
1.391E+07
0.045
769.674
75.470
3.039E+02
111.220
30.585
3.146E+05
785.667
235.700
Land use name

Residential-High
Density
ResidentialMedium Density
ResidentialMed/Low Density
Residential-Low
Density
Commercial
77
Table 7.5. Average annual yields per unit area of land uses in the Neshanic River Watershed
Land
use
Area (ac)
Water yield
(inch)
Sediment yield
(ton/ac)
TN
(lb/ac)
TP
(lb/ac)
URHD
92.269
30.676
0.125
11.068
1.166
URMD
190.970
25.866
0.033
5.843
0.722
URML
336.454
23.903
0.007
3.548
0.729
URLD
4899.210
17.724
0.002
1.923
0.374
UCOM
256.733
32.730
0.169
13.912
1.311
Institutional
UINS
451.266
30.027
0.099
9.667
1.034
Transportation
Agricultural LandGeneric
Corn
UTRN
149.051
36.516
0.477
25.324
2.527
AGRL
328.947
23.734
0.108
19.220
1.139
CORN
1834.412
24.055
0.078
60.584
1.585
Soybean
SOYB
1847.508
24.665
0.118
15.377
1.051
Rye
RYE
321.963
17.928
0.006
3.449
0.397
Hay
HAY
748.803
19.052
0.014
6.912
0.193
Timothy
TIMO
1671.273
19.591
0.013
9.999
0.229
Pasture
PAST
892.456
23.259
0.078
5.686
1.705
Orchard
ORCD
99.929
19.626
0.001
10.031
0.197
Forest-Deciduous
FRSD
3047.600
22.439
0.0005
2.763
0.073
Forest-Evergreen
FRSE
179.554
20.391
0.0001
4.678
0.085
Forest-Mixed
FRST
902.409
17.590
0.0001
2.252
0.070
Wetlands-Forested
WETF
1101.952
25.370
0.0002
11.523
0.081
Land use name

Residential-High
Density
Residential-Medium
Density
ResidentialMed/Low Density
Residential-Low
Density
Commercial
Wetlands-Mixed
WETL
139.718
27.419
0.0003
5.509
0.540
* The average water yield of urban lands is low due to the dominance of low density residential urban
land use and its relative low capacity of surface runoff generation.
78
Table 7.6. Average annual water yields of land uses in subbasins during 1997- 2008
Water yield (inch/yr)
Subbasin
Urban
Row crop
Other agriculture
Forest
Wetland
18.744
23.940
18.025
21.468
24.445
21.226
23.894
0.000
20.939
25.430
18.438
23.478
20.228
21.181
24.477
24.505
24.317
20.050
22.546
25.561
21.702
22.773
20.935
21.653
26.074
18.278
24.343
21.228
20.045
26.006
18.692
24.341
20.998
20.621
0.000
18.103
24.334
18.617
20.819
26.428
26.624
22.372
19.458
20.118
26.147
10
20.634
23.913
20.888
20.119
26.791
11
26.346
23.586
19.888
21.870
24.362
12
21.763
24.231
20.411
20.857
25.590
13
18.547
24.533
19.430
21.890
26.574
14
17.835
23.572
19.824
22.065
25.571
15
17.213
23.383
18.872
21.545
25.883
16
17.495
23.377
21.309
20.218
25.556
17
25.110
23.474
20.966
20.332
25.565
18
17.814
23.902
19.576
21.698
25.583
19
22.570
23.347
19.947
22.389
25.581
20
17.829
23.412
22.011
21.844
26.071
21
18.853
25.131
19.190
19.935
27.688
22
19.540
24.039
20.741
23.246
25.679
23
17.819
24.144
20.998
22.387
25.600
24
18.040
23.929
20.460
20.573
26.003
25
18.868
23.996
20.404
22.154
25.833
Watershed
20.396
23.835
20.433
21.291
25.600
7.2. Sediment Loading and Yields

7.2.1. Watershed Sediment Loading
The average annual sediment/TSS load discharged at the Neshanic River Watershed outlet (subbasin 16) is 1715.105 ton/year. Figure 7.2 shows the monthly TSS loads and variations obtained from the simulated daily loads during the period from 1997 to 2008. Average monthly loads vary from 6.014 (August) to 19.564 lb/ac (June), with two months
79
below 10 lb/ac (6.014 lb/ac in August and 9.246 lb/ac in November) and other ten months
having higher loads between 12.411 (May) and 19.564 lb/ac. Medians of monthly sediment loads are close to averages during January to March and December, and are 2.357
to 10.827 lb/ac lower for other months. Variations measured by the spans between the
25th and 75th percentiles are larger during January, April, June, July, September, November and December ranging from 12.143 (November) to 24.951 (October) lb/ac, compared
to other months from 6.623 (August) to 10.252 (February) lb/ac. The seasonal distribution of average monthly sediment loads generally follows the pattern of precipitation,
with larger variations during some monthly due to weather changes. Of course, land covers and streamflow also affect the seasonal distribution of stream flows.
Average
Median
25th Percentile
75th Percentile
35
TSS (lb/ac)
30
25
20
15
10
5
0
1
10
11
12
Month
Figure 7.2. Monthly TSS loads and variation at the watershed outlet during 1997-2008
7.2.2. Sediment Yields and Source Assessment
Annual sediment yields from subwatershed lands (Table 7.7) range from 0.008 (subbasin
8) to 0.079 (subbasin 16) ton/ac/yr, due to many combinations of types of land use/cover
and soil in this suburban watershed. Total sediment yields of subbasin lands range from
6.125 (subbasin 8) to 69.884 (subbasin 16) ton/yr, with only three subbasins having sediment yields more than 50 (subbasins 12, 16, 23) ton/yr. The total sediment yield of a
subbasin is the product of yield per unit area and land area in that subbasin. Sediment
contributions from reaches range from 0.367 (subbasin 22) to 208.337 (subbasin 16)
ton/yr, six of which have sediment yield more than 50 ton/yr. Note that reach sediment
contribution in each subbasin is the net sediment amount added when stream flow routines through the main channel with erosion and settling processes, and is calculated by
subtracting inflow load from outflow load. The spatial distributions of annual sediment
yields from the lands and reaches in subbasins are mapped in Figure 7.3 and Figure 7.4,
respectively. The Average annual sediment yield exported from the watershed outlet is
1715.105 ton/yr, 40.47% of which is from land yields, and 59.53% from reach contribution. This indicates that stream channel erosion is the major contributor to sediment loading in the watershed (Figure 7.5).
80
Table 7.7. Average annual sediment yields of subbasins during 1997- 2008
Area (ac)
Reach
drainage
areaa (ac)
Stream
discharge
(ft3/s)
Land
yield
(ton/ac/yr)
Land
yield
(ton/yr)
Reach
contributionb
(ton/yr)
Totalc
(ton/yr)
1480.161
1480.161
3.593
0.012
17.828
39.068
56.895
689.424
689.424
1.733
0.036
24.501
6.981
31.482
1082.322
1082.322
2.584
0.015
15.973
27.475
43.448
726.490
2891.133
7.290
0.048
34.758
16.498
51.255
333.592
1413.443
3.443
0.021
6.907
27.760
34.667
1109.503
3830.133
9.249
0.019
21.076
29.147
50.223
956.298
956.298
2.188
0.043
40.989
1.157
42.146
738.845
738.845
1.759
0.008
6.125
10.765
16.890
434.905
7141.346
17.687
0.051
22.375
56.402
78.777
10
580.698
580.698
1.401
0.026
14.809
2.169
16.977
11
879.695
14529.796
36.150
0.053
46.960
51.349
98.309
12
958.769
16061.850
39.938
0.058
55.494
161.121
216.615
13
555.987
555.987
1.325
0.027
14.861
4.224
19.084
14
622.706
17668.035
43.617
0.051
31.783
155.977
187.760
15
664.713
664.713
1.596
0.025
16.630
14.302
30.932
16
879.695
19521.325
47.887
0.079
69.884
208.337
278.221
17
652.358
6498.872
16.239
0.039
25.197
81.847
107.043
18
709.192
1373.906
3.308
0.014
9.992
17.288
27.280
19
625.177
5831.687
14.535
0.057
35.651
24.435
60.085
20
511.508
1885.414
4.632
0.057
29.340
22.662
52.002
21
995.835
995.835
2.280
0.023
22.471
8.304
30.775
22
654.829
654.829
1.673
0.032
20.691
0.367
21.059
23
1272.593
3335.923
8.346
0.045
56.769
33.226
89.995
24
775.911
2053.446
5.120
0.031
24.431
10.803
35.233
Subbasin
25
622.706
622.706
1.544
0.046
28.542
7.652
36.194
Wa19513.912 19521.325
47.887
0.036
694.034
1021.070
1715.105
tershed
a. A reach drainage area includes the containing subbasin area and all upstream subbasin areas.
b. Reach contribution is the net sediment amount added within a main channel through the erosion
and settling processes.
c. Total yield of a subbasin is the sum of yields from both land and main channel sources.
81
Figure 7.3. Annual sediment yields from lands in each subbasin
82
Figure 7.4. Annual sediment yields from reaches in each subbasin
83
Source contributions of average annual load for sediment
40.47%
Lands
Stream reaches
59.53%
Figure 7.5. Source contributions for sediment average annual load
The average annual sediment yields of land uses and per unit area of land uses in
the whole watershed are given in Table 7.4 and Table 7.5, respectively. Commercial, institutional, transportation, corn, soybean, pasture, and agricultural land-generic lands
yield 35.593 to 217.696 ton/yr, while other land uses have less sediment yields, in the
range of 0.023 to 22.316 ton/yr. The sediment yields from failing septic systems and cattle direct deposit are nil. Urban areas generally have high sediment yields per unit area,
especially the transportation zone with 0.477 ton/ac much higher than all of others.
Commercial, residential-high density, soybean, agricultural land-generic (rotation of soybean and corn), institutional, corn and pasture land uses have the next high sediment
loading rates ranging from 0.169 and 0.078 ton/ac in the descending order. Middle and
low density residential and other agricultural land uses have relative lower sediment loading rates between 0.002 and 0.033 ton/ac. Forests and wetlands have the lowest loading
rates below 0.0005 ton/ac.
Average annual sediment yields of grouped land uses in each subbasin and the watershed during 1997- 2008 are shown in Table 7.8. At the whole watershed level, annual
sediment yields of grouped urban, row crop, other agriculture, forest lands and wetlands
are 0.0299, 0.0918, 0.0302, 0.0004 and 0.0002 ton/ac/yr, respectively. Row crop lands
have higher yields varying from 0.0274 ton/ac/yr (subbasin 9) to 0.3305 ton/ac/yr (subbasin 13). Other agriculture and urban lands have medium yields varying from 0.0042
ton/ac/yr (subbasin 9) to 0.0656 ton/ac/yr (subbasin 16), and 0.0013 ton/ac/yr (subbasin
20) to 0.0962 ton/ac/yr (subbasin 9), respectively. Variations in sediment yields of these
three groups of land uses among subbasins are caused by the difference in compositions
of land uses and types of soils. Sediment yield variations of forests and wetlands are
small. Figure 7.6 presents the contributions of sediment average annual yield from different land uses.
84
Table 7.8. Average annual sediment yields of land uses in subbasins during 1997- 2008
Subbasin
Urban
Sediment yield (ton/ac/yr)

Other
Row crop
Forest
agriculture
0.2140
0.0076
0.0004
Wetland
0.0047
0.0113
0.1368
0.0000
0.0000
0.0001
0.0309
0.0525
0.0409
0.0002
0.0004
0.0685
0.0326
0.0072
0.0013
0.0000
0.0256
0.0781
0.0139
0.0001
0.0000
0.0070
0.0484
0.0262
0.0000
0.0001
0.0236
0.1494
0.0140
0.0003
0.0000
0.0028
0.0421
0.0143
0.0007
0.0002
0.0962
0.0274
0.0042
0.0000
0.0000
10
0.0215
0.0821
0.0287
0.0001
0.0000
11
0.0868
0.0712
0.0167
0.0002
0.0001
12
0.0542
0.0945
0.0470
0.0004
0.0001
13
0.0034
0.3305
0.0326
0.0016
0.0011
14
0.0018
0.1140
0.0279
0.0015
0.0001
15
0.0015
0.1168
0.0110
0.0006
0.0012
16
0.0015
0.1330
0.0656
0.0002
0.0000
17
0.0636
0.0667
0.0188
0.0000
0.0000
18
0.0015
0.0332
0.0249
0.0001
0.0000
19
0.0752
0.0768
0.0114
0.0004
0.0000
20
0.0013
0.1091
0.0281
0.0000
0.0001
21
0.0291
0.0684
0.0189
0.0003
0.0004
22
0.0091
0.0751
0.0408
0.0012
0.0005
23
0.0018
0.0763
0.0381
0.0005
0.0001
24
0.0106
0.0688
0.0197
0.0000
0.0000
25
0.0030
0.1505
0.0281
0.0007
0.0001
Watershed
0.0299
0.0918
0.0302
0.0004
0.0002
85
0.0003
Contributions of sediment average annual yield from

different land uses
0.25%
0.04%
14.87%
27.46%
Urban
Row crop
Other agriculture
Forest
Wetland
57.38%
Figure 7.6. Contributions of sediment average annual yield from different land uses
7.3. Nitrogen Loading and Yields

7.3.1. Watershed Nitrogen Loading
The average annual total nitrogen (TN) load discharged at the Neshanic River Watershed
outlet (subbasin 16) is 229134.145 lb/year. Figure 7.7 shows the monthly TN loads and
variations obtained from the simulated daily loads during the period from 1997 to 2008.
Average monthly loads vary from 0.244 (August) to 1.597 lb/ac (January), with five
months (June to October) below 1 lb/ac and other seven months having higher loads between 1.048 (May) and 1.597 lb/ac (January). Medians of monthly TN loads are close to
averages during March, August to October, and December; 0.131 lb/ac higher for January
and 0.156 lb/ac higher for February; and are 0.124 to 0.310 lb/ac lower for other months.
Variations measured by the spans between the 25th and 75th percentiles are larger during
January to April and October to December ranging from 0.847 (February) to 1.332 (December) lb/ac, compared to other months from 0.266 (August) to 0.771 (June) lb/ac. The
seasonal distribution of average monthly TN loads does not follows the pattern of precipitation, which shows a V shape with lower monthly loads during the growing months.
This indicates that increasing land vegetations greatly decrease nitrogen loads and TN
losses are larger during growing-off season due to nitrogens easy mobility in soils and
solubility in water.
86
Average
Median
25th Percentile
75th Percentile
2.5
TN (lb/ac)
2
1.5
1
0.5
0
1
10
11
12
Month
Figure 7.7. Monthly TN loads and variation at the watershed outlet during 1997-2008
7.3.2. Nitrogen Yields and Source Assessment
Annual TN yields from subwatershed lands (Table 7.9) range from 4.340 (subbasin 21) to
39.795 (subbasin 18) lb/ac/yr, due to many combinations of types of land uses/covers and
soils in this suburban watershed. Total TN yields of subbasins range from 28222.3 (subbasin 18) to 2594.786 (subbasin 5) lb/yr, with 8 subbasins (subbasins 18, 25, 24, 16, 23,
12, 9 and 6) having TN yields more than 10000 lb/yr. The total TN yield of lands in a
subbasin is the product of TN yield per unit area and land area in that subbasin. In addition to uplands, TN sources in a subbasin also include cattle direct deposit and failing
septic system effluents into its main reach and reach contribution due to nitrogen cycle
processes. Cattle direct deposits of subbasins vary from 0 to 24.289 lb/yr, while failing
septic effluents carry 0 to 105.138 lb/yr. TN contributions from reaches range from 164.061 (subbasin 18) to 1321.488 (subbasin 11) lb/yr, seven of which (subbasins 8, 13,
14, 16, 18 and 25) have negative TN contributions and other have position contributions.
Note that reach TN contribution in each subbasin is the net TN load added when stream
flow routines through the main channel with alga death and growth, nitrogen transform
and settling processes, and is calculated by subtracting inflow load from outflow load.
Many reaches have position TN contributions because of there are large amount of algae
flowing into stream together with surface runoff and their die-off provides the sources of
addition nitrogen input to the reach. The spatial distribution of annual TN yields from the
lands in subbasins is mapped in Figure 7.8. 97.84% of the average annual TN load in the
watershed is from land yields. Cattle direct deposit, septic systems, and reach contributions are only 0.05%, 0.34% and 1.77%. This indicates that fertilizer applications and
other overland practices are the dominant contributors to TN loading in the watershed
(Figure 7.9).
87
Table 7.9. Average annual TN yields of subbasins during 1997- 2008

Land yield
(lb/yr)
Cattle
direct
deposit
(lb/yr)
Septic
(lb/yr)
4.826
7143.728
0.000
86.022
62.483
7292.232
1.733
7.226
4981.458
0.000
23.895
4.777
5010.129
1082.322
2.584
5.149
5572.540
0.000
33.453
50.357
5656.350
726.490
2891.133
7.290
6.522
4737.935
0.000
9.558
441.494
5188.987
333.592
1413.443
3.443
7.778
2594.786
0.000
0.000
73.543
2668.328
1109.503
3830.133
9.249
9.890
10972.606
0.000
76.464
212.066
11261.136
956.298
956.298
2.188
5.783
5529.944
0.000
66.906
138.120
5734.970
738.845
738.845
1.759
8.369
6183.403
0.000
105.138
-39.334
6249.207
434.905
7141.346
17.687
26.911
11703.751
0.000
0.000
177.527
11881.278
10
580.698
580.698
1.401
6.063
3520.569
16.001
0.000
111.844
3648.414
11
879.695
14529.796
36.150
10.546
9277.072
4.743
4.779
1321.488
10608.081
12
958.769
16061.850
39.938
13.024
12487.463
9.707
28.674
283.110
12808.954
13
555.987
555.987
1.325
4.849
2695.854
3.151
47.790
-27.817
2718.977
14
622.706
17668.035
43.617
9.703
6041.861
0.000
28.674
-42.255
6028.280
15
664.713
664.713
1.596
6.236
4144.929
0.000
23.895
3.417
4172.241
16
879.695
19521.325
47.887
17.244
15169.301
17.552
4.779
-68.711
15122.921
17
652.358
6498.872
16.239
14.083
9187.337
24.289
23.895
153.956
9389.477
18
709.192
1373.906
3.308
39.795
28222.300
0.000
19.116
-164.061
28077.355
19
625.177
5831.687
14.535
14.089
8808.110
0.000
4.779
743.546
9556.435
20
511.508
1885.414
4.632
15.831
8097.482
13.740
4.779
63.181
8179.182
21
995.835
995.835
2.280
4.340
4321.706
0.000
62.127
97.003
4480.836
22
654.829
654.829
1.673
8.948
5859.582
7.535
4.779
58.068
5929.964
23
1272.593
3335.923
8.346
11.480
14608.848
6.817
66.906
159.064
14841.635
24
775.911
2053.446
5.120
20.259
15719.070
0.000
38.232
316.625
16073.927
25
622.706
622.706
1.544
26.667
16605.650
7.686
19.116
-49.604
16582.847
Watershed
19513.912
19521.325
47.887
11.489
224187.283
111.220
783.755
4051.887
229134.145
Reach drai- Stream

Land yield
nage areaa discharge
(lb/ac/yr)
3
(ac)
(ft /s)
Subbasin
Area (ac)
1480.161
1480.161
3.593
689.424
689.424
1082.322
Reach
contributio- Totalb (lb/yr)
na(lb/yr)
a. Reach contribution is the net amount added within a main channel through the algae growth, decay, settling and other instream processes.
b. Total yield of a subbasin is the sum of yields from both land and main channel contributions.
88
Figure 7.8. Annual nitrogen yields from lands in each subbasin
89
Source contributions of average annual load for TN

0.34%
1.77%
0.05%
Lands
Livestock access to
streams
Failing septic tanks
Stream reaches
97.84%
Figure 7.9. Source contributions for TN average annual load
The average annual TN yields of land uses and per unit area of land uses in the
whole watershed are given in Table 7.4 and Table 7.5, respectively. Corn, soybean, timothy, wetlands-forested, residential-low density, forest-deciduous, and agricultural landgeneric lands yield 111135.074 to 6322.259 lb/yr in the descending order, while other
land uses have less TN yields, in the range of 769.674 to 5175.374 lb/yr. The TN yields
from failing septic systems and cattle direct deposit are 783.755 and 111.22 lb/yr, respectively. Corn lands have high TN yields per unit area, with 60.584 lb/ac much higher than
all of others. Transportation, agricultural land-generic, soybean, commercial, wetlandsforested, residential-high density, orchard, timothy and institutional land uses have the
next high sediment loading rates ranging from 25.324 to 9.667 lb/ac in the descending
order. Other land uses have relative lower sediment loading rates between 1.923 and
6.912 lb/ac.
Average annual TN yields of grouped land uses in each subbasin and the watershed
during 1997- 2008 are shown in Table 7.10. At the whole watershed level, annual TN
yields of grouped urban, row crop, other agriculture, forest lands and wetlands are 3.836,
33.922, 8.194, 2.735 and 10.846 lb/ac/yr, respectively. Row crop lands have higher yields
varying from 13.444 lb/ac/yr (subbasin 3) to 165.859 lb/ac/yr (subbasin 18). Other agriculture lands and wetlands have medium yields varying from 6.937 lb/ac/yr (subbasin 18)
to 14.958 lb/ac/yr (subbasin 4), and 8.885 lb/ac/yr (subbasin 15) to 13.345ton/ac/yr (subbasin 5), respectively. TN yield variations of urban and forest lands are relative smaller.
Variations in TN yields of the groups of land uses among subbasins are caused by the difference in compositions of land uses and types of soils. Figure 7.10 presents the contributions of TN average annual yield from different land uses.
90
Table 7.10. Average annual nitrogen yields of land uses in subbasins during 1997- 2008
Subbasin
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
Watershed
Urban
1.711
Row crop
15.351
TN yield (lb/ac/yr)
Other agriculture
8.142
Forest
3.041
Wetland
10.937
3.120
20.806
0.000
3.060
9.768
4.375
13.444
7.197
3.192
10.930
6.104
18.379
14.958
2.407
12.346
5.286
13.639
8.280
3.628
13.345
2.423
22.676
8.302
2.043
10.855
2.305
20.393
9.401
1.851
0.000
1.816
37.148
7.386
2.057
10.109
8.049
134.553
11.555
2.334
9.982
3.519
20.341
7.919
2.160
10.153
7.467
18.334
9.182
2.090
8.950
5.348
30.471
9.201
1.790
12.328
1.808
18.452
9.121
3.289
11.510
2.316
16.911
8.721
2.387
12.344
1.659
17.421
6.139
2.091
8.885
1.504
35.121
7.355
1.626
12.346
6.394
67.653
7.877
2.422
12.345
5.632
165.859
6.937
5.389
12.754
10.147
18.354
10.259
2.019
12.339
3.540
27.095
7.291
3.108
10.130
3.033
15.343
7.772
2.510
10.981
2.913
21.463
8.081
2.017
8.926
2.254
18.909
8.705
2.019
10.505
3.009
46.084
8.297
3.702
11.016
1.926
97.186
7.707
2.109
9.862
3.836
33.922
8.194
2.735
10.846
91
Contributions of TN average annual yield from

different land uses
6.01%
10.91%
5.04%
Urban
12.47%
Row crop
Other agriculture
Forest
Wetland
65.57%
Figure 7.10. Contributions of TN average annual yield from different land uses
7.4. Phosphorus Loading and Yields

7.4.1. Watershed Phosphorus Loading
The average annual total phosphorus (TP) load discharged at the Neshanic River Watershed outlet (subbasin 16) is 12287.089 lb/year. Figure 7.11 shows the monthly TP
loads and variations obtained from the simulated daily loads during the period from 1997
to 2008. Average monthly loads vary from 0.025 (August) to 0.073 lb/ac (June), with
three months (February, August and November) below 0.05 lb/ac and other months having higher loads between 0.05 (January and May) and 0.073 lb/ac (June). Medians of
monthly TP loads are close to averages during January to March, July to September, November and December; lower 0.013 to 0.039 lb/ac for other months. Variations measured
by the spans between the 25th and 75th percentiles are larger during January, April, June,
September and October and December ranging from 0.054 (January) to 0.074 (June)
lb/ac, compared to other months from 0.027 (May) to 0.042 (July) lb/ac. The seasonal
distribution of average monthly TP loads generally follows the pattern of precipitation.
This trend is different from that of TN, which should be due to phosphoruss immobility
in soils, relative smaller solubility in water and its strong adsorbability to sediment. Of
course, land covers and streamflow also affect the seasonal distribution of TP loads.
92
Average
Median
25th Percentile
75th Percentile
0.12
TP (lb/ac)
0.1
0.08
0.06
0.04
0.02
0
1
10
11
12
Month
Figure 7.11. Monthly TP loads and variation at the watershed outlet during 1997-2008
7.4.2. Phosphorus Yields and Source Assessment
Annual TP yields from subwatershed lands (Table 7.11) range from 0.233 (subbasin 1) to
0.960 (subbasin 16) lb/ac/yr, due to many combinations of types of land uses/covers and
soils in this suburban watershed. Total TP yields of subbasins range from 153.371 (subbasin 5) to 862.847 (subbasin 23) lb/yr, with 10 subbasins (subbasins 23,16, 12, 11, 25,
24, 6, 7, 17 and 18) having TN yields more than 500 lb/yr. The total TP yield of lands in
a subbasin is the product of TP yield per unit area and land area in that subbasin. In addition to uplands, TP sources in a subbasin also include cattle direct deposit and failing septic system effluents into its main reach and reach contribution due to phosphorus cycle
processes. Note that reach TP contribution in each subbasin is the net TP load added
when stream flow routines through the main channel with alga death and growth, nitrogen transform and settling processes, and is calculated by subtracting inflow load from
outflow load. 24 out of 25 reaches have position TP contributions because of there are
large amount of algae flowing into stream together with surface runoff and their die-off
provides the sources of addition phosphorus input to the reach. The spatial distribution of
annual TP yields from the lands in subbasins is mapped in Figure 7.12. 92.84% of the
average annual TP load in the watershed is from land yields. Cattle direct deposit, septic
systems, and reach contributions are only 0.25%, 1.91%, and 5.00%. This indicates that
fertilizer applications and other overland practices are the dominant contributors to TP
loading in the watershed (Figure 7.13).
93
Table 7.11. Average annual TP yields of subbasins during 1997- 2008

Cattle
direct
deposit
(lb/yr)
Septic
(lb/yr)
344.538
0.000
25.807
27.098
397.444
0.562
387.491
0.000
7.168
17.802
412.462
2.584
0.319
345.333
0.000
10.036
35.347
390.717
2891.133
7.290
0.551
400.455
0.000
2.867
65.220
468.542
333.592
1413.443
3.443
0.460
153.371
0.000
0.000
27.135
180.506
1109.503
3830.133
9.249
0.499
553.258
0.000
22.939
40.418
616.615
956.298
956.298
2.188
0.558
533.669
0.000
20.072
26.088
579.828
738.845
738.845
1.759
0.393
290.538
0.000
31.541
15.083
337.163
434.905
7141.346
17.687
0.838
364.253
0.000
0.000
44.827
409.080
10
580.698
580.698
1.401
0.623
361.989
4.400
0.000
31.269
397.658
11
879.695
14529.796
36.150
0.705
620.260
1.304
1.434
6.981
629.979
12
958.769
16061.850
39.938
0.786
753.414
2.669
8.602
46.848
811.533
13
555.987
555.987
1.325
0.412
229.098
0.866
14.337
6.375
250.676
14
622.706
17668.035
43.617
0.581
361.586
0.000
8.602
-8.451
361.738
15
664.713
664.713
1.596
0.400
266.099
0.000
7.168
11.519
284.787
16
879.695
19521.325
47.887
0.960
844.253
4.827
1.434
29.395
879.908
17
652.358
6498.872
16.239
0.815
531.562
6.680
7.168
44.460
589.869
18
709.192
1373.906
3.308
0.719
509.795
0.000
5.735
15.157
530.686
19
625.177
5831.687
14.535
0.734
458.741
0.000
1.434
0.000
460.174
20
511.508
1885.414
4.632
0.862
440.689
3.779
1.434
21.936
467.837
21
995.835
995.835
2.280
0.376
374.190
0.000
18.638
24.049
416.877
22
654.829
654.829
1.673
0.479
313.337
2.072
1.434
26.805
343.647
23
1272.593
3335.923
8.346
0.678
862.847
1.875
20.072
39.316
924.109
24
775.911
2053.446
5.120
0.711
551.743
0.000
11.470
9.811
573.023
25
622.706
622.706
1.544
0.891
554.519
2.114
5.735
19.327
581.695
Watershed
19513.912
19521.325
47.887
0.585
11407.028
30.585
235.126
614.350
12287.089
Reach drai- Stream

Land yield Land yield
nage areaa dis-charge
(lb/ac/yr)
(lb/yr)
3
(ft /s)
(ac)
Subbasin
Area (ac)
1480.161
1480.161
3.593
0.233
689.424
689.424
1.733
1082.322
1082.322
726.490
Reach contributiona Totalb (lb/yr)

(lb/yr)
a. Reach contribution is the net amount added within a main channel through the algae growth, decay, settling and other instream
processes.
b. Total yield of a subbasin is the sum of yields from both land and main channel contributions.
94
Figure 7.12. Annual phosphorus yields from lands in each subbasin
95
Source contributions of average annual load for TP

1.91%
5.00%
0.25%
Lands
Livestock access to
streams
Stream reaches
92.84%
Figure 7.13. Source contributions for TP average annual load
The average annual TP yields of land uses and per unit area of land uses in the
whole watershed are given in Table 7.4 and Table 7.5, respectively. Corn, soybean, residential-low density and pasture lands yield 2907.535 to 1521.275 lb/yr in the descending
order, while other land uses have less TP yields, in the range of 15.186 to 466.571 lb/yr.
The TP yields from failing septic systems and cattle direct deposit are 235.126 and
30.585 lb/yr, respectively. Transportation lands have high TP yields per unit area, with
2.527 lb/ac much higher than all of others. Pasture, corn, commercial, residential-high
density, agricultural land-generic, soybean, institutional land uses have the next high sediment loading rates ranging from 1.705 to 1.034 lb/ac in the descending order. Other
land uses have relative lower sediment loading rates between 0.070 and 0.729 lb/ac.
Average annual TP yields of grouped land uses in each subbasin and the watershed
during 1997- 2008 are shown in Table 7.12. At the whole watershed level, annual TP
yields of grouped urban, row crop, other agriculture, forest lands and wetlands are 0.550,
1.235, 0.606, 0.073 and 0.133 lb/ac/yr, respectively. Row crop lands have higher yields
varying from 0.800 lb/ac/yr (subbasin 4) to 2.546 lb/ac/yr (subbasin 18). Other agriculture and urban ands have medium yields varying from 0.197 lb/ac/yr (subbasin 9) to
1.192 lb/ac/yr (subbasin 20), and 0.201 lb/ac/yr (subbasin 20) to 0.935 ton/ac/yr (subbasin 9), respectively. TP yield variations of forests and wetlands are relative small. Variations in TP yields of the groups of land uses among subbasins are caused by the difference in compositions of land uses and types of soils. Figure 7.14 presents the contributions of TP average annual yield from different land uses.
96
Table 7.12. Average annual phosphorus yields of land uses in subbasins during 1997- 2008
Subbasin
TP yield (lb/ac/yr)
Urban
Row crop
Other agriculture
Forest
Wetland
0.460
1.404
0.206
0.064
0.071
0.574
1.113
0.000
0.060
0.190
0.589
1.005
0.815
0.062
0.070
0.713
0.800
0.207
0.105
0.085
0.576
1.136
0.513
0.082
0.086
0.399
0.972
0.608
0.072
0.185
0.443
1.251
0.436
0.071
0.000
0.379
1.107
0.226
0.091
0.233
0.935
2.152
0.197
0.066
0.278
10
0.535
1.135
1.022
0.067
0.092
11
0.875
1.051
0.403
0.067
0.196
12
0.714
1.208
0.807
0.067
0.085
13
0.452
1.561
0.682
0.099
0.098
14
0.352
1.083
0.321
0.085
0.085
15
0.458
1.237
0.294
0.067
0.084
16
0.378
1.329
0.947
0.076
0.085
17
0.775
1.557
1.041
0.080
0.085
18
0.201
2.546
0.460
0.069
0.075
19
0.856
0.988
0.214
0.067
0.085
20
0.201
1.159
1.192
0.063
0.255
21
0.477
0.926
0.203
0.067
0.157
22
0.530
0.951
0.516
0.111
0.085
23
0.348
0.993
0.631
0.067
0.085
24
0.535
1.321
0.447
0.062
0.191
25
0.481
2.449
0.578
0.105
0.245
Watershed
0.550
1.235
0.606
0.073
0.133
97
Contributions of TP average annual yield from

different land uses
1.45%
2.64%
18.16%
30.77%
Urban
Row crop
Other agriculture
Forest
Wetland
46.99%
Figure 7.14. Contributions of TP average annual yield from different land uses
7.5. Fecal Coliform Loading and Yields
The current bacteria model of SWAT2005 does not provide accurate monthly and annual
outputs for bacteria loads or concentrations at hru, subbasin and reach levels. Though daily bacteria loads for reaches are correct as confirmed with communication with the model
developers. Therefore average annual fecal coliform and E. coli yields of land uses and
subbasins are not given in this report. The daily bacteria loads at the watershed outlet
were utilized to compute monthly and annual bacteria loads for the whole watershed.
Nevertheless, some general observations were obtained during the modeling.
7.5.1. Watershed Fecal Coliform Loading
The average annual fecal coliform (FC) loading discharged at the Neshanic River Watershed outlet (subbasin 16) is 1.535E+14 cfu/year, or equivalently 7.865E+09 cfu/ac.
Figure 7.15 shows the monthly fecal coliform loads and variations obtained from the simulated daily loads during the period from 1997 to 2008. Average monthly loads vary
from 3.224E+08 (February) to 2.667E+09 cfu/ac (April), with eleven months (except for
April) below 109 cfu/ac between 3.224E+08 (February) and 6.592E+08 cfu/ac (October).
Medians of monthly stream flow are close to averages except for April when median is
2.031E+09 cfu/ac lower than average. Variations measured by the spans between the 25th
and 75th percentiles are 4.244E+08 cfu/ac during April which is larger than other months
ranging from 9.648E+06 (January) to 1.745E+08 (July) cfu/ac. The seasonal distribution
of average monthly fecal coliform loads does not follows the pattern of precipitation,
which indicates the surface runoff sources are not dominate in the watershed. On the contract, cattle direct deposit and failing septic system effluents are the major contributors.
The exceptional high peak of fecal coliform load during April is consistent with the as-
98
sumption that all manure applications occur in that month. Larger variations for April
among years are due to the variable precipitations in different years.
Average
Median
25th Percentile
75th Percentile
3.0E+09
FC (cfu/ac)
2.5E+09
2.0E+09
1.5E+09
1.0E+09
5.0E+08
0.0E+00
1
10
11
12
Month
Figure 7.15. Monthly fecal coliform loads and variation at the watershed outlet during
1997-2008
7.5.2. Fecal Coliform Yields and Source Assessment

The total fecal coliform yield of lands in a subbasin is the product of fecal coliform
yield per unit area and land area in that subbasin. In addition to uplands, fecal coliform
sources in a subbasin also include cattle direct deposit and failing septic system effluents
into its main reach. Cattle direct deposits of subbasins vary from 0 to 9.073E+12 cfu/yr,
with 15 subbasins (subbasins 1 to 9, 14, 15, 18,19, 21 and 24) having no cattle direct deposit and other subbasins are in the range of 1.177E+12 (subbasin 13) to 9.073E+12
(subbasin 17) cfu/yr. Fecal coliform loads from failing septic effluents vary from 0 to
1.192E+13 cfu/yr, with 3 subbasins (subbasins 5, 9 and 10) having no septic input and
other subbasins are in the range of 5.419E+11 (subbasin 22) to 1.192E+13 (subbasin 8)
cfu/yr. Fecal coliform contributions from reaches are not calculated because the current
version of SWAM only output outflow bacteria loads of reaches. The spatial distributions
of annual fecal coliform loads from cattle direct deposits and failing septic systems are
mapped in Figure 7.16 and Figure 7.17, respectively. As shown in Figure 7.18 the major
source contributions of average annual load for fecal coliform are from manure application, cattle direct deposits and failing septic effluents, occupying 31.34%, 18.90% and
45.94%, respectively. Since there are some issues with the latest version of SWAT2005,
the monthly and annual output results of bacteria yields from HRUs and loads at subbasin
outlets are not reliable. The bacteria contributions were estimated as the differences of
watershed loads of the baseline scenario and corresponding operation removal scenarios.
Sensitivity analyses indicate that even the original estimates of the deer and goose densities are increased to ten times, the load from animal grazing is still negligible compared
to septic and cattle direct deposits. Therefore, to reduce fecal coliform loads in the watershed, measures should focus on the control of manure application, cattle direct deposits
and failing septic effluents into streams.
99
Table 7.13. Average annual fecal coliform yields of subbasins during 1997- 2008
Subbasin
Area (ac)
Reach drainage
areaa (ac)
Stream discharge (ft3/s)
Cattle direct
deposit (cfu/yr)
Septic
(cfu/yr)
1480.161
1480.161
3.593
0.000E+00
9.755E+12
689.424
689.424
1.733
0.000E+00
2.710E+12
1082.322
1082.322
2.584
0.000E+00
3.794E+12
726.490
2891.133
7.290
0.000E+00
1.084E+12
333.592
1413.443
3.443
0.000E+00
0.000E+00
1109.503
3830.133
9.249
0.000E+00
8.671E+12
956.298
956.298
2.188
0.000E+00
7.587E+12
738.845
738.845
1.759
0.000E+00
1.192E+13
434.905
7141.346
17.687
0.000E+00
0.000E+00
10
580.698
580.698
1.401
5.977E+12
0.000E+00
11
879.695
14529.796
36.150
1.772E+12
5.419E+11
12
958.769
16061.850
39.938
3.626E+12
3.252E+12
13
555.987
555.987
1.325
1.177E+12
5.419E+12
14
622.706
17668.035
43.617
0.000E+00
3.252E+12
15
664.713
664.713
1.596
0.000E+00
2.710E+12
16
879.695
19521.325
47.887
6.557E+12
5.419E+11
17
652.358
6498.872
16.239
9.073E+12
2.710E+12
18
709.192
1373.906
3.308
0.000E+00
2.168E+12
19
625.177
5831.687
14.535
0.000E+00
5.419E+11
20
511.508
1885.414
4.632
5.133E+12
5.419E+11
21
995.835
995.835
2.280
0.000E+00
7.045E+12
22
654.829
654.829
1.673
2.815E+12
5.419E+11
23
1272.593
3335.923
8.346
2.546E+12
7.587E+12
24
775.911
2053.446
5.120
0.000E+00
4.335E+12
25
622.706
622.706
1.544
2.871E+12
2.168E+12
Watershed
19513.912
19521.325
47.887
4.155E+13
8.888E+13
100
Figure 7.16. Annual fecal coliform yields from cattle direct deposits in subbasins
101
Figure 7.17. Annual fecal coliform yields from failing septic systems in subbasins
102
Source contributions of average annual load for

fecal coliform
1.37%
2.46%
31.34%
45.94%
Livestock access to
streams
Manure application
Livestock grazing
Wildlife
18.90%
Figure 7.18. Source contributions of average annual load for fecal coliform
7.6. E. coli Loading and Yields

7.6.1. Watershed E. Coli Loading
The average annual E. coli (EC) loading discharged at the Neshanic River Watershed outlet (subbasin 16) is 9.632E+13 cfu/year, or equivalently 4.937E+09 cfu/ac. Figure 7.19
shows the monthly E. coli loads and variations obtained from the simulated daily loads
during the period from 1997 to 2008. Average monthly loads vary from 2.031E+08 (February) to 1.671E+09 cfu/ac (April), with eleven months (except for April) below 109
cfu/ac between 2.009E+08 (February) and 4.115E+08 cfu/ac (October). Medians of
monthly stream flow are close to averages except for April when median 1.272E+09
cfu/ac lower than average. Variations measured by the spans between the 25th and 75th
percentiles are 2.658E+08 cfu/ac during April which is larger than other months ranging
from 5.979E+06 (January) to 1.095E+08 (July) cfu/ac. The seasonal distribution of average monthly E. coli loads does not follows the pattern of precipitation, which indicates
the surface runoff sources are not dominate in the watershed. On the contract, cattle direct
deposit and failing septic system effluents are the major contributors for E. coli loading.
The exceptional high peak of E. coli load during April is consistent with the assumption
that all manure applications occur in that month. Larger variations for April among years
are due to the variable precipitations in different years.
103
Average
Median
25th Percentile
75th Percentile
1.8E+09
1.6E+09
EC (cfu/ac)
1.4E+09
1.2E+09
1.0E+09
8.0E+08
6.0E+08
4.0E+08
2.0E+08
0.0E+00
1
10
11
12
Month
Figure 7.19. Monthly E. coli loads and variation at the watershed outlet during 1997-2008
7.6.2. E. Coli Yields and Source Assessment
The total E. coli yield of lands in a subbasin is the product of E. coli yield per unit area
and land area in that subbasin. In addition to uplands, E. coli sources in a subbasin also
include cattle direct deposit and failing septic system effluents into its main reach. Cattle
direct deposits of subbasins vary from 0 to 5.671E+12 cfu/yr, with 15 subbasins (subbasins 1 to 9, 14, 15, 18,19, 21 and 24) having no cattle direct deposit and other subbasins
are in the range of 7.355E+11 (subbasin 13) to 5.671E+12 (subbasin 17) cfu/yr. E. coli
loads from failing septic effluents vary from 0 to 7.511E+12 cfu/yr, with 3 subbasins
(subbasins 5, 9 and 10) having no septic input and other subbasins are in the range of
3.414E+11 (subbasin 22) to 7.511E+12 (subbasin 8) cfu/yr. E. coli contributions from
reaches are not calculated because the current version of SWAM only output outflow
bacteria loads of reaches. The spatial distributions of annual E. coli loads from cattle direct deposit and failing septic system are mapped in Figure 7.20 and Figure 7.21, respectively. As shown in Figure 7.22 the major source contributions of average annual load for
E. coli are from manure application, cattle direct deposits and failing septic effluents, occupying 31.25%, 18.81% and 46.09%, respectively. Sensitivity analyses indicate that
even the original estimates of the deer and goose densities are increased to ten times, the
load from animal grazing is still negligible compared to septic and cattle direct deposits.
Therefore, to reduce E. coli loads in the watershed, measures should focus on the control
of manure application, cattle direct deposits and failing septic effluents into streams.
It should be reminded that the modeling results of bacteria loads rely on estimates
of related sources, which is a very difficult task due to no enough statistic data about wild
life distribution densities and bacteria contents in manures nevertheless to say data in a
specific watershed. The uses of bacteria modeling results are most sound in comparing
relative reduction effects of BMPs.
104
Table 7.14. Average annual E. coli yields of subbasins during 1997- 2008
Subbasin
Area (ac)
Reach drainage
areaa (ac)
Stream discharge (ft3/s)
Cattle direct
deposit (cfu/yr)
Septic
(septic/yr)
1480.161
1480.161
3.593
0.000E+00
6.145E+12
689.424
689.424
1.733
0.000E+00
1.707E+12
1082.322
1082.322
2.584
0.000E+00
2.390E+12
726.490
2891.133
7.290
0.000E+00
6.828E+11
333.592
1413.443
3.443
0.000E+00
0.000E+00
1109.503
3830.133
9.249
0.000E+00
5.463E+12
956.298
956.298
2.188
0.000E+00
4.780E+12
738.845
738.845
1.759
0.000E+00
7.511E+12
434.905
7141.346
17.687
0.000E+00
0.000E+00
10
580.698
580.698
1.401
3.736E+12
0.000E+00
11
879.695
14529.796
36.150
1.107E+12
3.414E+11
12
958.769
16061.850
39.938
2.266E+12
2.048E+12
13
555.987
555.987
1.325
7.355E+11
3.414E+12
14
622.706
17668.035
43.617
0.000E+00
2.048E+12
15
664.713
664.713
1.596
0.000E+00
1.707E+12
16
879.695
19521.325
47.887
4.098E+12
3.414E+11
17
652.358
6498.872
16.239
5.671E+12
1.707E+12
18
709.192
1373.906
3.308
0.000E+00
1.366E+12
19
625.177
5831.687
14.535
0.000E+00
3.414E+11
20
511.508
1885.414
4.632
3.208E+12
3.414E+11
21
995.835
995.835
2.280
0.000E+00
4.438E+12
22
654.829
654.829
1.673
1.759E+12
3.414E+11
23
1272.593
3335.923
8.346
1.592E+12
4.780E+12
24
775.911
2053.446
5.120
0.000E+00
2.731E+12
25
622.706
622.706
1.544
1.794E+12
1.366E+12
Watershed
19513.912
19521.325
47.887
2.597E+13
5.599E+13
105
Figure 7.20. Annual E. coli yields from cattle direct deposits in subbasins
106
Figure 7.21. Annual E. coli yields from failing septic systems in subbasins
107
Source contributions of average annual load for E. coli

1.40%
2.45%
31.25%
46.09%
Livestock access to
streams
Manure application
Livestock grazing
Wildlife
18.81%
Figure 7.22. Source contributions of average annual load for E. coli
7.7. TMDL Targets

7.7.1. TMDL and Load Duration Curve
A Total Maximum Daily Load (TMDL) is a calculation of the maximum amount of a

pollutant that a water body can receive and still meet water quality standards, and an allocation of that amount to the pollutant's sources. A TMDL is the sum of the allowable
loads of a single pollutant from all contributing point and nonpoint sources. The calculation must include a margin of safety to ensure that the water body can be used for the
purposes the State has designated. The calculation must also account for seasonable variation in water quality. A TMDL is defined by the simple equation:
TMDL = LC =WLA+LA +MoS + RC
where: TMDL = total maximum daily load; LC = loading capacity; WLA = wasteload
allocation for point sources; LA = load allocation for nonpoint sources; MoS = margin of
safety; and RC = reserve capacity.
A modified loading capacity (LC') can be defined as:
LC'= LC MoS RC =WLA+LA
Since it incorporates both RC and MoS implicitly or explicitly through reduced water quality targets, LC' is equal to the total maximum daily load allocated among all point
and nonpoint sources.
It is important to recognize that LC' is sometimes expressed as an average daily
load based upon average long term flow conditions. These long term average TMDLs
108
have been dubbed as bare bones TMDLs due to the simplicity of the calculation and
their lack of usefulness. While these TMDLs seem to satisfy the requirements of the
Clean Water Act, they have contributed little to any watershed/water body assessment
and restoration plans. These types of TMDLs do little to characterize the problems the
TMDLs are intended to address. Without adequate characterizations, appropriate solutions cannot be identified and implemented.
For TMDLs to be more beneficial in the assessment and implementation process,
TMDLs should reflect adequate water quality across flow conditions rather than at a single flow event such as average daily flow. Many states have begun to use load duration
curves as a more robust method for setting TMDL targets. It is also a useful tool for better characterizing the pollutant problems over the entire flow regime. A duration curve is
a graph representing the percentage of time during which the value of a given parameter
(e.g. flow, load) is equaled or exceeded. Such a graph can be easily generated using a
spreadsheet computer program. The following presents the steps involved in developing a
load duration curve.
Step 1. Develop Flow Duration Curve:
Using available daily streamflow data, a flow duration curve is developed for the
site in question. Data for the curve is generated by: 1) ranking the daily flow data from
highest to lowest; 2) calculating percent of days these flows were exceeded (= rank
number of data points).
Step 2. Develop Load Duration Curve:
The load duration curve is developed by multiplying the ranked stream flows by the water
quality standard for the parameters under examination and by a conversion factor. To apply a
10% margin of safety (MOS), the results are divided by 1.1. In this case, a 10% MOS was
selected to account for uncertainties in the gauged flow data.
Step 3. Plot Water Quality Sample Data on Load Duration Curve:

In order to compare water quality sample data to the load duration curve, the first task is to
calculate daily loads for each sample using the pollutant concentration and stream flow for
the particular day. Next, the flow values for each day are compared to the flow duration curve
data in order to determine the value for Percent of Days Flow Exceeded which is equivalent to Percent of Days Load Exceeded. These load and percent data points are then plotted
on the load duration curve. Points above the curve represent exceedances of the water standards and the associated allowable loadings.
Use of Load Duration Curves in Assessments and TMDLs
A load duration curve has a number of uses and benefits:
The load duration curve approach is useful for characterizing the problem and
providing a visual display for people to better understand the problem and the
109
TMDL targets. With the load duration curves, the frequency and magnitude of
the water quality standards and allowable loads are easily presented. The magnitude of loading reduction can be better understood.
Load duration curves can be used to characterize flow conditions under which
standard exceedances are occurring. In general, exceedances that occur in the 0
to 10% area of the curve may be considered to represent unique high flow problems that may exceed feasible management remedies. Exceedances in the 99 to
100% reflect extreme drought conditions.
Different loading mechanisms can dominate at different flow regimes. The load
duration curve can be used to begin differentiating between nonpoint source and
point source problems. In general, exceedances of the load duration curve during
the higher flows can be indicative of nonpoint source problems. Exceedances
during the lower flows can be indicative of point source problems. However,
each water body must be considered on a case by case basis.
Load duration curves can show seasonal water quality effects. Data points that
cluster within a narrow range of the percent of load exceeded can be associated
with the season when that range of flows typically occur.
Water quality conditions between multiple reaches and watersheds can be examined through the comparison of load duration curves at different sites.
Using the load duration as a TMDL target. TMDLs can be developed which set
load limitations over the entire flow range, not just for an annual average. With
this type of target, the goal of the TMDL may be to reduce the number of samples exceeding the load duration curve (or TMDL target) to less than 10% for the
period of concern.
It should be recognized that not only there are uncertainties with the water quality
standards and the associated load duration curves, but one must critically consider the use
of the less than 10% exceedance threshold as the TMDL goal. While these value is
commonly used by many states in their assessments, actual allowable exceedance frequency could be more or need to be less than 10% for the beneficial uses, depending
upon the particular water body and pollutant.
7.7.2. TMDL Targets of the Neshanic River watershed
The TMDL targets for the Neshanic River Watershed in this plan is defined as the total
pollutant loadings that satisfy the water quality at the watershed outlet. A 10% safety
margin and less than 10% exceedance threshold were adopted to determine the targets.
The time period of load duration curves shown in Figure 7.23 to Figure 7.37 are 19972008. The load duration curves of TSS, TN and TP based on measured data at the Reaville station indicate that nonpoint sources are dominate in the watershed, since the trend
that loads increase with stream flows are very apparent. This kind of increasing trend of
fecal coliform and E. coli in the load duration curves based on measured data at the Reaville station is not distinct, and many observed loads during medium and low flows are as
high as those during high flow conditions. This phenomenon indicates that there are point
sources are the major contributors for bacteria, which should be the direct deposit of ma110
nures from cattle and failing septic effluents. The same trends are followed for the load
duration curves obtained with simulated data at the watershed outlet. The almost flat
bands of simulated loads in the duration curves of fecal coliform and E. coli are the results of the simplified assumption that input from direct deposit of failing septic effluent
into streams remain constant through the year and cattle direct deposits remain constant
during grazing period.
The frequencies of TMDL exceedances and target reduction percentage at the Reaville station and watershed outlet are given in Table 7.15. The measured flow and concentration data at Reaville indicate that frequencies of TMDL exceedances for TSS, TN,
TP, FC and EC are 7.32%, 0, 30.49%, 37.50% and 59.02%, respectively. TSS and TN
satisfy the TMDL goal of less than 10% exceedance threshold, while the loads of TP,
fecal coliform and E. coli need to be reduced by 48%, 90% and 91% according the targets
at Reaville. The simulated results at the watershed outlet are comparable to those at Reaville due to the short distance from it. The frequencies of TMDL exceedances for TSS,
TN, TP, FC and EC at the outlet are 12.25%, 1.76%, 37.96%, 60.96% and 63.38%, respectively. The target reductions at the watershed outlet are 9% for TSS, 49% for TP, 89
for Fecal coliform and E. coli.
Table 7.15. Frequencies of TMDL exceedances and target reduction percentages
Frequencies of exceedances
Target reduction
Simulated at
Simulated at
Measured at Simulated at
Measured at Simulated at
watershed
watershed
Pollutant
Reaville (N1) Reaville (N1)
Reaville (N1) Reaville (N1)
outlet
outlet
TSS
7.32%
8.30%
12.25%
0
0
9%
TN
0
2.03%
1.76%
0
0
0
TP
30.49%
38.49%
37.96%
48%
48%
49%
FC
37.50
61.15%
60.96%
90%
90%
89%
EC
59.02%
63.91%
63.38 %
91%
91%
89%
111
TSS load duration curve 1997-2008, Station N1

1000.000
Load duration curve (at water quality standard)
Load duration curve (with 10% margin of safety)
Actual loads as sampled
TSS load (ton/day)
100.000
10.000
1.000
0.100
0.010
0.001
0%
10%
20%
30%
40%
50%
60%
70%
80%
90%
100%
Percent of days load exceeded
Figure 7.23. TSS load duration curve at Reaville (N1) based on measured data
TN load duration curve 1997-2008, Station N1

1000000.000
100000.000
TN load (lb/day)
10000.000
1000.000
100.000
10.000
1.000
0.100
0.010
0.001
0%
10%
20%
30%
40%
50%
60%
70%
80%
90%
100%
Figure 7.24. TN load duration curve at Reaville (N1) based on measured data
112
TP load duration curve 1997-2008, Station N1

10000.000
1000.000
TP load (lb/day)
100.000
10.000
1.000
0.100
0.010
0.001
0%
10%
20%
30%
40%
50%
60%
70%
80%
90%
100%
Figure 7.25. TP load duration curve at Reaville (N1) based on measured data
FC load duration curve 1997-2008, Station N1

1.E+16
1.E+15
FC load (cfu/day)
1.E+14
1.E+13
1.E+12
1.E+11
1.E+10
1.E+09
1.E+08
1.E+07
0%
10%
20%
30%
40%
50%
60%
70%
80%
90%
100%
Figure 7.26. Fecal coliform load duration curve at Reaville (N1) based on measured data
113
EC load duration curve 1997-2008, Station N1

1.0E+16
1.0E+15
EC load (cfu/day)
1.0E+14
1.0E+13
1.0E+12
1.0E+11
1.0E+10
1.0E+09
1.0E+08
1.0E+07
0%
10%
20%
30%
40%
50%
60%
70%
80%
90%
100%
Figure 7.27. E. coli load duration curve at Reaville (N1) based on measured data
TSS load duration curve 1997-2008, Station N1

1000.000
Load duration curve (with 10% marginl of safety)
Simulated loads with SWAT
TSS load (ton/day)
100.000
10.000
1.000
0.100
0.010
0.001
0%
10%
20%
30%
40%
50%
60%
70%
80%
90%
100%
Figure 7.28. TSS load duration curve at Reaville (N1) based on simulation
114
TN load duration curve 1997-2008, Station N1

1000000.000
100000.000
TN load (lb/day)
10000.000
1000.000
100.000
10.000
1.000
0.100
0.010
0.001
0%
10%
20%
30%
40%
50%
60%
70%
80%
90%
100%
Figure 7.29. TN load duration curve at Reaville (N1) based on simulation
TP load duration curve 1997-2008, Station N1

10000.000
1000.000
TP load (lb/day)
100.000
10.000
1.000
0.100
0.010
0.001
0%
10%
20%
30%
40%
50%
60%
70%
80%
90%
100%
Figure 7.30. TP load duration curve at Reaville (N1) based on simulation
115
FC load duration curve 1997-2008, Station N1

1.E+15
FC load (cfu/day)
1.E+14
1.E+13
1.E+12
1.E+11
1.E+10
0%
10%
20%
30%
40%
50%
60%
70%
80%
90%
100%
Figure 7.31. Fecal coliform load duration curve at Reaville (N1) based on simulation
EC load duration curve 1997-2008, Station N1

1.0E+16
1.0E+15
EC load (cfu/day)
1.0E+14
1.0E+13
1.0E+12
1.0E+11
1.0E+10
1.0E+09
1.0E+08
1.0E+07
0%
10%
20%
30%
40%
50%
60%
70%
80%
90%
100%
Figure 7.32. E. coli load duration curve at Reaville (N1) based on simulation
116
TSS load duration curve 1997-2008, watershed outlet

1000.000
TSS load (ton/day)
100.000
10.000
1.000
0.100
0.010
0.001
0%
10%
20%
30%
40%
50%
60%
70%
80%
90%
100%
Figure 7.33. TSS load duration curve at watershed outlet based on simulation
TN load duration curve 1997-2008, watershed outlet

1000000.000
100000.000
TN load (lb/day)
10000.000
1000.000
100.000
10.000
1.000
0.100
0.010
0.001
0%
10%
20%
30%
40%
50%
60%
70%
80%
90%
100%
Figure 7.34. TN load duration curve at watershed outlet based on simulation
117
TP load duration curve 1997-2008, watershed outlet

10000.000
1000.000
TP load (lb/day)
100.000
10.000
1.000
0.100
0.010
0.001
0%
10%
20%
30%
40%
50%
60%
70%
80%
90%
100%
Figure 7.35. TP load duration curve at watershed outlet based on simulation
FC load duration curve 1997-2008, watershed outlet

1.E+15
FC load (cfu/day)
1.E+14
1.E+13
1.E+12
1.E+11
1.E+10
0%
10%
20%
30%
40%
50%
60%
70%
80%
90%
100%
Figure 7.36. Fecal coliform load duration curve at watershed outlet based on simulation
118
EC load duration curve 1997-2008, watershed outlet

1.0E+16
1.0E+15
EC load (cfu/day)
1.0E+14
1.0E+13
1.0E+12
1.0E+11
1.0E+10
1.0E+09
1.0E+08
1.0E+07
0%
10%
20%
30%
40%
50%
60%
70%
80%
90%
100%
Figure 7.37. E. coli load duration curve at watershed outlet based on simulation
119
7.8. Critical Areas of Pollutant Loads Reduction
Based on analysis about simulated pollutant yields from land uses in subbasins and reach
contributions, and estimates of cattle direct deposits and failing septic system effluents,
grouped land use areas and reaches are classified into five categories for each kind of
loads according their yields per unit area and loads directly added to reaches. The results
are summarized in Table 7.16, in which the lower the rank the higher the priority is. Category I represent the highest priority areas for load reduction; II the next priority; and so
on. Both classes I and II may be considered as critical areas for pollutant loads reduction.
Since bacteria yields from wetlands were not simulated in the model, they are excluded
from classification for bacteria loading in the table.
The ranks were not classified for specific subbasins but for land uses, because the
same type of land use areas generally have similar yields per unit area regardless the difference in soil types. Furthermore, this assignment should eliminate the inaccurate or inappropriate simulation results for specific locations caused by uncertain factors or imperfect model calibration.
Table 7.16. Land classification for load reduction
Other
Forest Wetland
agriculture
II
IV
V
III
V
II
II
V
IV
Load
Urban
Row crop
TSS
TN
TP
III
IV
III
I
I
I
FC
IV
II (manure III (grazing

application
pasture
areas)
lands)
EC
IV
II (manure III (grazing

application
pasture
areas)
lands)
120
Reach
I (all reaches)
V
V
I (reaches with
cattle deposit
and septic effluent)
I (reaches with
cattle deposit
and septic effluent)
8. BMP Scenarios
8.1. Definition of BMP Scenarios
The calibrated SWAT model was applied to analyze twenty scenarios of potential best
management practice options in order to reduce pollutant loads by putting them at the
lands use sources, overland pathways and stream channels. These BMP scenarios are defined in Table 8.1, in which a BMP was applied to all applicable lands or channels across
the whole watershed. Each management option was considered alone in one of the eleven
single-focus management scenarios, and then combinations of effective individual management options were investigated.
8.1.1. Single-focus Management Scenarios
The baseline scenario (S0) represents the existing land use management conditions in the
watershed, which is characterized by modest fertilizer applications and minimum tillage
(chisel plow and disk plow). In addition to the baseline, the following eleven single-focus
scenarios with individual BMPs were evaluated:
Scenario S1 Reduce manure application
Manure application is one of the major bacteria sources in the Neshanic River watershed.
The application rates of cattle and horse manures to corn lands were reduced from 45
Mg/ha in baseline scenario to 11.6 Mg/ha.
Scenario S2 Grazing management
Over grazing can lead to poor land covers and cause severe soil loss. To preserve certain
amount of grass on the land, the minimal dry grass biomass to be left on pasture lands
was increased from 200 kg/ha in baseline scenario to 700 kg/ha. It was assumed that
grazing stopped once the minimal grass biomass limit was reached, and animals would be
fed with hays harvested from other lands.
Scenario S3 Nitrogen commercial fertilizer management
This scenario involves reducing nitrogen commercial fertilizer application rates by 25%
from existing levels, for all agricultural lands and urban lawns.
Scenario S4 Phosphorus commercial fertilizer management
This scenario involves reducing phosphorus commercial fertilizer application rates by

25% from existing levels, for all agricultural lands and urban lawns.
Scenario S5 Phosphorus commercial fertilizer management
Phosphorus commercial fertilizer application rates were reduced by 25% for all agricultural lands from existing levels, and by 100% for urban lawns.
121
Scenario S6 No Tillage
Minimum tillage (chisel plow and disk plow) was already applied as a conservation tillage approach to row crop land uses (AGRL, corn, soybean, and rye) in the watershed.
This scenario investigated going to a very low tillage approach on row crops, with only
one no-tillage operation prior to planting each year. No-till agriculture involves the
amount, orientation and distribution of crop and other plant residue on the soil surface
year round while limiting soil-disturbing activities to only those necessary to place nutrients, condition residue and plant crops. No-till reduces sheet and rill and wind erosion,
slows down surface runoff and peak runoff, increases infiltration and reduces surface runoff by increasing land cover and surface roughness, and works to improve soil organic
matter content. To represent this scenario, the no-till operation in SWAT model was applied and SCS curve numbers (CN) was reduced by three percent. Overland Mannings
roughness coefficients (OV_N) and biomass mixing factor (BIOMIX) were increased to
0.3 and 0.4, respectively. USLE cover factors (USLE_C) were decreased to be 0.03 for
corn, soybean and corn-soybean rotation fields, and 0.01 for rye lands.
Scenario S7 Cover crop
Cover crops were represented with SWAT by scheduling a crop rotation within a single
year. Notice that SWAT does not allow growing of two crops in a single HRU simultaneously. The cover crop BMP was simulated by planting winter rye following crop harvest and killing winter rye by crop planting for corn-soybean rotation (AGRL), corn and
soybean lands.
Scenario S8 Filter strips
Field borders are installed along the perimeter of a field to reduce sediment, nutrients,
pesticides, and bacteria in surface runoff as it passes through the edge-of-the-field vegetative strip. Pollutant loads in surface runoff are trapped in the strip of vegetation. The
function of filter strips is similar to the field borders except filter strips are installed along
the edge of a channel segment. Properly designed filter strips or riparian buffers provide
effective strategy for removing pollutants in surface runoff from agricultural lands. In this
scenario, 5-m (15-ft) filter strips were assumed to be applied to all agricultural lands.
The previous versions of SWAT provided a specific method to incorporate filter
strips through the FILTERW parameter defined in an HRU that reflects the width of the
strip (Neitsch et al., 2005). The trapping efficiency for sediment, nutrients and pesticides
is calculated:
trapef 0.367 ( width filtstrip ) 0 .2967
where trapef is the fraction of the constituent loading trapped by the filter strip, and
widthfiltstrip is the width of the filter strip (m).
The filter strip trapping efficiency for bacteria (Moore et al., 1988) is calculated:
122
trapef ,bact
(12 4.5width filtstrip )

100
where trapef,bact is the fraction of the bacteria loading trapped by the filter strip, and
widthfiltstrip is the width of the filter strip (m).
However, filter strips utilizing these experience functions were disabled in recent
versions of SWAT2005 due to the prospect to develop a process-based filter strips function. In order to simulate filter strips, the pollutant yields from lands and loads at the watershed outlet output generated the model under various scenarios were simply deducted
from baseline scenario with removal rates estimated utilizing the removal efficiencies
obtained using the prescribed experience functions, 59.16% for TSS, TN and TP, and
34.50%for bacteria.
Scenario S9 Fencing
The model includes loads from direct deposit of cattle manure into streams, input as point
sources. This scenario simulated the elimination of direct deposit by constructing fences
for all pasture lands close to streams.
Scenario S10 Eliminate failing septic tanks
The model includes loads from failing septic tanks, input as point sources. This scenario
simulated the elimination of failing septic tanks by re-estimating the failure rate changed
to zero. This was assumed to be accomplished by improving the maintenance of septic
systems and increase the reliability.
Scenario S11 Channel protection
Many segments in the watershed are subject to channel erosion. The channel protection
practice is to cover channel segment with erosion resistant material to reduce gully erosion. This scenario evaluated the benefits of reducing channel erosion by increased vegetative cover of channel banks or the stabilization using riprap. In the model, the channel erodibility (CH_EROD) was reduced from 0.01 to 0.001 in all subbasins. Here a
small number (i.e. 0.001) was used instead of zero to avoid the default values set by
SWAT. The channel cover factor (CH_COV) was adjusted to 0.5, and channel Mannings roughness coefficients were set to 0.02 according to Arabi et al. (2008).
8.1.2. Combinational Management Scenarios
Normally full compliance with TMDL target annual load reductions and daily exceedance frequencies is hard to be achieved by applying just one kind of BMPs. None of
the single-focus scenarios produces satisfied load reduction. Thus, a combination of several of the more promising management options needs to be pursued.
123
Scenario S12 Combo 1
This scenario was constructed to reduce sediment, TN, TP and bacteria loads by combining the BMPs tested in S1 (reduce manure), S2 (grazing management), S3 (nitrogen fertilizer management), S4 (phosphorus fertilizer management), S7 (cover crop), S9 (fencing), and S10 (eliminating septic failure).
This scenario was constructed to reduce sediment, TN, TP and bacteria loads by combining the BMPs tested in S1 (reduce manure), S2 (grazing management), S3 (nitrogen fertilizer management), S4 (phosphorus fertilizer management), S8 (filter strips), S9 (fencing), and S10 (eliminating septic failure).
This scenario was constructed to reduce sediment, TN, TP and bacteria loads by combining the BMPs tested in S1 (reduce manure), S2 (grazing management), S3 (nitrogen fertilizer management), S4 (phosphorus fertilizer management), S7 (cover crop), S8 (filter
strips), S9 (fencing), and S10 (eliminating septic failure).
This scenario was constructed to reduce sediment, TN, TP and bacteria loads by combining the BMPs tested in S1 (reduce manure), S2 (grazing management), S3 (nitrogen fertilizer management), S4 (phosphorus fertilizer management), S7 (cover crop), S8 (filter
strips), S9 (fencing), S10 (eliminating septic failure), and S11 (channel protection).
This scenario was designed to evaluate the effectiveness of major promising BMPs for
TP load reduction by combining the BMPs tested in S7 (cover crop) and S8 (filter strips).
TP load reduction by combining the BMPs tested in S4 (phosphorus fertilizer management), S7 (cover crop) and S8 (filter strips).
bacteria load reductions by combining the BMPs tested in S1 (reduce manure), and S9
(fencing).
124
bacteria load reductions by combining the BMPs tested in S1 (reduce manure), S8 (filter
strips), and S9 (fencing).
bacteria load reductions by combining the BMPs tested in S1 (reduce manure), S8 (filter
strips), S9 (fencing), and S10 (eliminating septic failure).
125
Table 8.1. Definition of BMP scenarios

Scenario
BMPs
S0
Baseline
S1
Reduce manure application
S2
Grazing management
S3
S4
S5
Nitrogen commercial
fertilizer management
Phosphorus commercial
Phosphorus commercial
S6
No tillage
S7
Cover crop
S8
Filter strips
S9
Fencing
S10
Eliminate failing septic

tanks
S11
Channel protection
S12
S13
S14
S15
S16
S17
S18
S19
S20
Combo 1
Combo 2
Combo 3
Combo 4
Combo 5
Combo 6
Combo 7
Combo 8
Combo 9
Description
The baseline scenario is characterized with modest N and P
commercial fertilizer applications and reduced tillage for agricultural lands. Cattle and horse manures are applied to 11% of
corn lands at standard rates. Tillage operations include: minimum (chisel/disk) plows for corn, soybean and rye; 6-year rotation moldboard/disk/hallow plows for timothy, hay and pasture.
AGRL is modeled as 2-year rotation of corn and soybean. Orchards, forests, and wetlands are modeled using their default
SWAT schedules.
Reduce application rates of cattle and horse manures to corn
lands from 45 Mg/ha to 11.6 Mg/ha.
Increase the minimal grass biomass of pasture lands from 200
kg/ha to 700 kg/ha to reduce soil erosion cause by over grazing.
Reduce N commercial fertilizer application rates by 25% for all
agricultural lands and urban lawns.
Reduce P commercial fertilizer application rates by 25% for all
agricultural lands and urban lawns.
Reduce P commercial fertilizer application rates by 25% for all
agricultural lands and by 100% for urban lawns.
Change to no-till operations for all row crop lands (AGRL, corn,
soybean, and rye).
Plant winter rye following crop harvest and kill winter rye by
crop planting for AGRL, corn and soybean lands.
Apply 5-m (15-ft) filter strips to all agricultural lands.
Construct fences for all pasture lands within 100 meters of a
stream.
Improve the maintenance of septic systems and increase the reliability. Assume 0% failing rate after improvement.
Increased vegetative cover of channel banks or the stabilization
using riprap.
Combination of BMPs in S1, S2, S3, S4, S7, S9, S10
Combination of BMPs in S1, S2, S3, S4, S8, S9, S10
Combination of BMPs in S1, S2, S3, S4, S7, S8, S9, S10
Combination of BMPs in S1, S2, S3, S4, S7, S8, S9, S10, S11
Combination of BMPs in S7, S8
Combination of BMPs in S4, S7, S8
Combination of BMPs in S1, S9
Combination of BMPs in S1, S8, S9
Combination of BMPs in S1, S8, S9, S10
126
8.2. Load Reductions of BMP Scenarios

8.2.1. Single-focus BMP Scenario Results
Average annual pollutant yields from grouped land uses, direct loads to streams, watershed average annual loads and reduction percentages, and daily load exceedance frequencies at the watershed outlet under BMP scenarios are summarized are in Table 8.2 to
Table 8.6.
In general, no tillage, cover crop, filter strips and channel protection are effective
BMPs for sediment removal, which lead to watershed average annual load reduction of
9.80, 15.21, 17.28 and 59.60 percent compared to baseline scenario. Reducing channel
erosion has a large impact on TSS loads. With each individual of these BMPs applied to
appropriate lands across the watershed, the target daily load exceedance frequency less
than 10 percent can be satisfied.
TN is not an issue as to satisfy its TMDL goal in the watershed even under the
baseline scenario. The simulations indicate that reducing manure application, nitrogen
fertilizer management, cover crop and filter strips are effective measures for TN reduction all with removal percentages more than 10 percent. No tillage operations reduce the
TN average annual load only 2.46 percent. The relative small reduction is primarily because the existing tillage practices already high conservation levels.
For TP load reduction, reduce manure application, phosphorus fertilizer management, cover crop and filter strips are more effective than other BMPs, with average annual load reduction percentages of 4.44, 15.36, 15.77 and 35.72 percent, respectively.
Edge-of-field filter strips provide the greatest reduction since they can be applied to all
agricultural lands and function throughout the year. However, the daily load exceedance
frequencies with these individual BMP applications are still more than the goal 10%.
Note that, the exceedance frequency for filter strop scenario is marked as less than
37.96%, due to the prescribed reason that the filter function is not simulated in the current
version of SWAT2005. Although the yields and loads can be reduced by applying estimated removal rates of filter strips, the reductions of daily exceedance frequencies cannot
be computed.
Bacteria pollution in the watershed is relative severe and need large reductions of
source loads. The scenario modeling shows that reducing manure application, filter strips,
fencing, eliminate failing septic tanks, and channel protection are effective measure for
both fecal coliform and E. coli load reductions, with reduction percentages of 23.23,
11.91, 19.30, 46.92 and 4.05 percent for fecal coliform, and 23.17, 11.88, 19.22, 47.09
and 4.05 percent for E. coli, respectively. However, daily exceedance frequencies are
high with each individual of these BMPs applied to the watershed, which are more than
30% even when it is assumed that no failing septic tanks exist.
One may observe that there are some negative load reduction percentages given in
the tables. These negative reductions mean that the corresponding loads actually increased. This is because the coupled overland and instream process models in SWAT in127
deed have affections to each other. For example, the decrease application of phosphorus
fertilizer while maintaining existing nitrogen fertilizer application will increase the ratio
of N:P components that received by lands, and result in more loss of nitrogen since it
cannot be taken by vegetation.
8.2.2. Combinational BMP Scenario Results
Since application of individual BMPs such as no tillage, cover crop, filter strips and
channel protection can reduce sediment load to satisfy daily exceedance frequency target,
the combinational scenarios of effective BMPS were designed to evaluate the possibility
to meet the goals for TP and bacteria. For TP, a combination of major effective BMPs,
reducing phosphorus fertilizer application rates, cover crop, and filter strips will lead to a
51.07 percent reduction of average annual load, which is more than the target 49%. Combination of only cover crop and filter strips will not achieve the target. With addition
BMPs including grazing management, reducing manure and nitrogen fertilizer applications, fencing, eliminating septic failure, and channel protection will have a larger reduction of load amounting to 51.86 percent. However, this small more reduction is cost inefficient compared to the combination of reducing phosphorus fertilizer application rates,
cover crop, and filter strips.
To satisfy the target reduction of bacteria loads, a combination of effective BMPS
including at least reducing manure application, filter strips, fencing, and eliminating septic failure is needed. This lest combination reduce average annual load by 92.49 percent
for fecal coliform and 92.51 percent for E. coli. With addition BMPs including grazing
management, nitrogen and phosphorus fertilizer applications, cover crop, and channel
protection will increase small reductions of load amounting to 94.45 percent for fecal coliform and 94.47 percent for E. coli. The daily exceedance frequencies of both fecal and
E. coli meet the target less than 10 percent for any BMP combination consisting reducing
manure application, filter strips, fencing, and eliminating septic failure.
128
Table 8.2. Reductions of sediment yields and loads under BMP scenarios
Direct load to
stream (ton/yr)
Yield from land (ton/ac/yr)

Scenario
S0
S1
S2
S3
S4
S5
S6
S7
S8*
S9
S10
S11
S12
S13*
S14*
S15*
S16*
S17*
S18
S19*
S20*
Urban
Row
crop
Other
agriculture
Forest
0.0299
0.0299
0.0299
0.0305
0.0299
0.0337
0.0299
0.0299
0.0299
0.0299
0.0299
0.0299
0.0305
0.0305
0.0305
0.0305
0.0299
0.0299
0.0299
0.0299
0.0299
0.0918
0.0917
0.0918
0.0918
0.0918
0.0918
0.0205
0.0383
0.0375
0.0918
0.0918
0.0918
0.0391
0.0374
0.0160
0.0160
0.0156
0.0156
0.0917
0.0375
0.0375
0.0302
0.0302
0.0164
0.0318
0.0302
0.0302
0.0302
0.0302
0.0123
0.0302
0.0302
0.0302
0.0175
0.0072
0.0072
0.0072
0.0123
0.0123
0.0302
0.0123
0.0123
0.0004
0.0004
0.0004
0.0004
0.0004
0.0004
0.0004
0.0004
0.0004
0.0004
0.0004
0.0004
0.0004
0.0004
0.0004
0.0004
0.0004
0.0004
0.0004
0.0004
0.0004
Watershed outlet load
Wetland
Cattle
direct
deposit
Septic
effluent
Average
annual
load
(ton/yr)
Load
reduction
percentage
(%)
Daily load
exceedance
frequency
(%)
0.0002
0.0002
0.0002
0.0002
0.0002
0.0002
0.0002
0.0002
0.0002
0.0002
0.0002
0.0002
0.0002
0.0002
0.0002
0.0002
0.0002
0.0002
0.0002
0.0002
0.0002
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
1715.105
1714.186
1667.981
1727.414
1715.105
1742.019
1547.002
1454.316
1418.678
1715.105
1715.105
692.986
1303.575
1285.820
1167.944
290.872
1295.241
1295.160
1714.186
1418.099
1298.866
0.05
2.75
-0.72
0.00
-1.57
9.80
15.21
17.28
0.00
0.00
59.60
23.99
25.03
31.90
83.04
24.48
24.49
0.05
17.32
24.27
12.25
12.21
11.36
12.25
12.25
12.55
9.51
7.76
<12.25
12.25
12.25
2.30
5.86
<10.75
<5.86
<1.12
<7.76
<7.76
12.21
<12.21
<11.43
129
Table 8.3. Reductions of TN yields and loads under BMP scenarios

Direct load to
stream (lb/yr)
Yield from land (lb/ac/yr)

Scenario
S0
S1
S2
S3
S4
S5
S6
S7
S8*
S9
S10
S11
S12
S13*
S14*
S15*
S16*
S17*
S18
S19*
S20*
Urban
Row
crop
Other
agriculture
Forest
3.836
3.836
3.836
3.418
3.836
19.900
3.836
3.836
3.836
3.836
3.836
3.836
3.418
3.418
3.418
3.418
3.836
3.836
3.836
3.836
3.836
33.922
20.354
33.922
30.073
33.916
33.916
31.965
21.605
13.325
32.630
33.922
33.922
7.158
6.548
2.849
2.849
8.468
8.465
20.354
8.312
8.312
8.194
8.194
7.592
6.239
8.194
8.194
8.194
8.194
3.333
8.161
8.194
8.194
5.728
2.239
2.239
2.239
3.201
3.201
8.194
3.346
3.346
2.735
2.735
2.735
2.735
2.735
2.735
2.735
2.735
2.735
2.735
2.735
2.735
2.735
2.735
2.735
2.735
2.735
2.735
2.735
2.735
2.735
Wetland
Cattle
direct
deposit
Septic
effluent
Average
annual
load (lb/yr)
10.846
10.846
10.846
10.846
10.846
10.846
10.846
10.846
10.846
10.846
10.846
10.846
10.846
10.846
10.846
10.846
10.846
10.846
10.846
10.846
10.846
111.220
111.220
111.220
111.220
111.220
111.220
111.220
111.220
111.220
0.000
111.220
111.220
0.000
0.000
0.000
0.000
111.220
785.667
111.220
785.667
0.000
783.755
783.755
783.755
783.755
783.755
783.755
783.755
783.755
783.755
783.755
0.000
783.755
0.000
0.000
0.000
0.000
783.755
111.220
783.755
0.000
783.755
229134.145
170345.495
227224.391
203711.356
229534.284
331470.155
223491.597
176363.012
123260.342
229049.635
228468.165
232924.810
102193.444
87237.938
71584.473
72425.960
102257.689
102312.065
170249.593
101530.117
100733.697
130
Load reduction
percentage
(%)
25.66
0.83
11.10
-0.17
-44.66
2.46
23.03
46.21
0.04
0.29
-1.65
55.40
61.93
68.76
68.39
55.37
55.35
25.70
55.69
56.04
Daily load
exceedance
frequency
(%)
1.76
0.34
1.78
1.00
1.76
13.00
1.21
0.62
<1.62
1.76
1.76
1.78
0.00
<0.07
0.00
0.00
<0.55
<0.55
0.34
<0.34
<0.34
Table 8.4. Reductions of TP yields and loads under BMP scenarios

Direct load to
stream (lb/yr)
Yield from land (lb/ac/yr)

Scenario
S0
S1
S2
S3
S4
S5
S6
S7
S8*
S9
S10
S11
S12
S13*
S14*
S15*
S16*
S17*
S18
S19*
S20*
Urban
Row
crop
Other
agriculture
Forest
0.550
0.550
0.550
0.613
0.412
0.221
0.550
0.550
0.550
0.550
0.550
0.550
0.472
0.472
0.472
0.472
0.550
0.412
0.550
0.550
0.550
1.235
1.100
1.235
1.231
1.036
1.036
1.274
0.773
0.504
1.235
1.235
1.235
0.511
0.366
0.209
0.209
0.316
0.257
1.100
0.449
0.449
0.606
0.606
0.549
0.633
0.529
0.529
0.606
0.606
0.247
0.606
0.606
0.606
0.492
0.201
0.201
0.201
0.247
0.216
0.606
0.247
0.247
0.073
0.073
0.073
0.073
0.073
0.073
0.073
0.073
0.073
0.073
0.073
0.073
0.073
0.073
0.073
0.073
0.073
0.073
0.073
0.073
0.073
Wetland
Cattle
direct
deposit
Septic
effluent
Average
annual
load (lb/yr)
0.133
0.133
0.133
0.133
0.133
0.133
0.133
0.133
0.133
0.133
0.133
0.133
0.133
0.133
0.133
0.133
0.133
0.133
0.133
0.133
0.133
30.585
30.585
30.585
30.585
30.585
30.585
30.585
30.585
30.585
0.000
30.585
30.585
0.000
0.000
0.000
0.000
30.585
235.700
30.585
235.700
0.000
235.126
235.126
235.126
235.126
235.126
235.126
235.126
235.126
235.126
235.126
0.000
235.126
0.000
0.000
0.000
0.000
235.126
30.585
235.126
0.000
235.126
12287.089
11741.445
12099.696
12764.765
10400.307
9096.273
13010.955
10349.601
7897.635
12261.383
12085.014
12182.370
8266.409
6599.333
5964.142
5915.103
7143.257
6012.446
11719.399
7676.055
7475.809
131
Load
reduction
percentage (%)
4.44
1.53
-3.89
15.36
25.97
-5.89
15.77
35.72
0.21
1.64
0.85
32.72
46.29
51.46
51.86
41.86
51.07
4.62
37.53
39.16
Daily load
exceedance
frequency
(%)
37.96
36.46
37.58
38.60
33.45
28.04
43.44
30.80
<37.96
37.37
35.75
37.76
22.56
<29.93
<22.56
<22.36
<30.80
<26.17
36.09
<36.09
<34.43
Table 8.5. Reductions of fecal coliform loads under BMP scenarios

Direct load to stream (cfu/yr)
Scenario
S0
S1
S2
S3
S4
S5
S6
S7
S8*
S9
S10
S11
S12
S13*
S14*
S15*
S16*
S17*
S18
S19*
S20*
Cattle direct
deposit
Septic
effluent
4.155E+13
4.155E+13
4.155E+13
4.155E+13
4.155E+13
4.155E+13
4.155E+13
4.155E+13
4.155E+13
0.000E+00
4.155E+13
4.155E+13
0.000E+00
0.000E+00
0.000E+00
0.000E+00
4.155E+13
8.909E+13
4.155E+13
8.909E+13
0.000E+00
8.888E+13
8.888E+13
8.888E+13
8.888E+13
8.888E+13
8.888E+13
8.888E+13
8.888E+13
8.888E+13
8.888E+13
0.000E+00
8.888E+13
0.000E+00
0.000E+00
0.000E+00
0.000E+00
8.888E+13
4.155E+13
8.888E+13
0.000E+00
8.888E+13

Load
Daily load
Average
reduction
exceedance
annual load
percentage
frequency
(cfu/yr)
(%)
(%)
1.535E+14
60.96
1.178E+14
23.23
60.57
1.533E+14
0.12
60.94
1.528E+14
0.39
60.99
1.534E+14
0.00
60.96
1.530E+14
0.31
60.89
1.656E+14
-7.90
59.84
1.518E+14
1.04
62.79
1.352E+14
11.91
<60.96
1.238E+14
19.30
51.22
8.145E+13
46.92
32.56
1.472E+14
4.05
59.73
1.504E+13
90.20
0.18
9.485E+12
93.82
<0.25
9.123E+12
94.05
<0.18
8.522E+12
94.45
<0.16
1.336E+14
12.95
<62.79
1.336E+14
12.95
<62.79
8.818E+13
42.53
50.67
8.354E+13
45.56
<50.67
1.153E+13
92.49
<0.25
132
Table 8.6. Reductions of E. coli loads under BMP scenarios

Direct load to stream (cfu/yr)
Scenario
Cattle direct
deposit
Septic
effluent
S0
S1
S2
S3
S4
S5
S6
S7
S8*
S9
S10
S11
S12
S13*
S14*
S15*
S16*
S17*
S18
S19*
S20*
2.597E+13
2.597E+13
2.597E+13
2.597E+13
2.597E+13
2.597E+13
2.597E+13
2.597E+13
2.597E+13
0.000E+00
2.597E+13
2.597E+13
0.000E+00
0.000E+00
0.000E+00
0.000E+00
2.597E+13
5.613E+13
2.597E+13
5.613E+13
0.000E+00
5.599E+13
5.599E+13
5.599E+13
5.599E+13
5.599E+13
5.599E+13
5.599E+13
5.599E+13
5.599E+13
5.599E+13
0.000E+00
5.599E+13
0.000E+00
0.000E+00
0.000E+00
0.000E+00
5.599E+13
2.597E+13
5.599E+13
0.000E+00
5.599E+13
Watershed outlet load (cfu/yr)

Load
Daily load
Average
reduction
exceedance
annual load
percentage
frequency
(cfu/yr)
(%)
(%)
9.632E+13
63.38
7.400E+13
23.17
63.08
9.621E+13
0.12
63.40
9.595E+13
0.39
63.56
9.632E+13
0.00
63.38
9.603E+13
0.31
63.40
1.039E+14
-7.88
62.15
9.532E+13
1.04
65.16
8.488E+13
11.88
<63.38
7.781E+13
19.22
54.96
5.097E+13
47.09
34.20
9.242E+13
4.05
61.76
9.412E+12
90.23
0.23
5.933E+12
93.84
<0.27
5.707E+12
94.07
<0.23
5.329E+12
94.47
<0.21
8.388E+13
12.92
<65.16
8.388E+13
12.92
<65.16
5.549E+13
42.39
54.48
5.258E+13
45.41
<54.48
7.213E+12
92.51
<0.27
9. Conclusions
The SWAT2005 model was reasonably calibrated and validated in the Neshanic River
Watershed, a suburban watershed in Central New Jersey, for the baseline land
use/management scenario. DEM, land use, soil, long term monitored weather data and
estimated manure application and literature bacteria content data were utilized to build
the model, while long term monitored daily stream flows at the Reaville USGS station
and water quality data from grabbed samples at the USGS station and the seven project
sites were used for calibration and validation purpose.
During the modeling period 1997-2008, simulated annual total stream flow at the
watershed outlet is 1.51E+9 ft3 or equivalent 21.318 inches of precipitation, with monthly
stream flows varying from 0.876 to 2.172 inches, about 24% to 66% of observed monthly
precipitation. The hydrological water balance analysis shows that more than 50% of
losses in the watershed are through evapotranspiration during dry years while less than
50% during wet years. Surface runoff dominates water yield no matter in a wet or dry
year. Base flow (30%~45%) mainly contributed from groundwater discharges and is an
important component of the total discharge within the study area that compliment to the
surface runoff.
133
The baseline simulation indicates that the main pollutant sources for sediment are
stream channels, row crops and other agricultural lands. Row crops, other agricultural
lands, and urban areas are main sources for TN and TP, while failing septic tanks, cattle
direct deposit into steams, manure applications are the major sources for fecal coliform
and E. coli loads. It was believed that the SWAT model, by considering land and soil
characteristics and pollutant movement on the lands and in the water, gave more realistic
load estimates than empirical models for nonpoint sources loading estimation. Load duration curves were developed for pollutants at the watershed outlet based on baseline scenario simulation. The target reductions for TSS, TP, fecal coliform and E. coli were estimated to be 9, 48, 89 and 89 percent, respectively, to meet the water quality goal with
less than 10% daily exceedance frequencies during 1997- 2008. TN is not an issue according to the water quality standard for nitrate.
Twenty BMP scenarios were simulated for the watershed to derive the effects of
BMP implementation would have on water quality at the outlet of watershed. Among the
eleven individual BMPs considered, filter strips are overall the most effective in reducing
loadings for all pollutants from overland sources. Eliminating septic failure and fencing
are the two key BMPs to reduce direct deposits of bacteria loads into streams. To meet
the water quality goal of less than 10% daily exceedance frequencies, any individual
BMPs of no tillage, cover crop, filter strips or channel protection would work for sediment reduction. For TP, a combination consisting effective BMPs, reducing phosphorus
fertilizer application rates, cover crop, and filter strips provided satisfied reduction, while
a combination of effective BMPS including at least reducing manure application, filter
strips, fencing, and eliminating septic failure is needed to meet the target reductions of
fecal coliform and E. coli loads.
In summary, in spite of the coarse nature of model setup for bacteria simulation and
the limited water quality monitoring data available for model calibration and validation,
this SWAT modeling study produced valuable quantitative information on the effectiveness of BMPs in reducing pollutant loads and improving water quality.
134
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Appendix A.
Management Schedules for Crops and Lawns
Table A.1. Schedule of management operations for corn under the baseline scenario
Date
4/10
4/15
4/15
4/15
4/17
5/10
5/10
5/10
5/10
6/1
Operation
Tillage
Fertilizer
Pesticide
Pesticide
Tillage
Planting
Fertilizer
Fertilizer
Fertilizer
Pesticide
6/15
Pesticide
7/15
Pesticide
Type
Chisel plow
Anhydrous ammonia*
Atrazine
Prowl
Disk
Regular Corn
N granule
P2O5
K2O
Bicep or lumax
Distinct or Banvel or Clarity or Celebrity Plus
Headline or Warrior fungicide
Rate
130 lbs/ac N
10.5 lbs/ac N
31.5 lbs/ac P
9 lbs/ac K
10/15
Harvest and kill
* Cow and horse manures are applied to 9 corn HRUs, both at the rates of 45,000 kg/ha.
Table A.2. Schedule of management operations for soybean under the baseline scenario
Date
5/1
5/20
5/27
5/27
5/27
6/15
10/15
Operation
Tillage
Tillage
Planting
Fertilizer
Fertilizer
Pesticide
Harvest and kill
Type
Chisel
Disk
Regular Soybean
P2O5
K2O
Classic or First rate
Rate
25 lbs/ac P
70 lbs/ac K
Table A.3. Schedule of management operations for rye under the baseline scenario
Date
3/15
4/20
7/1
10/8
10/8
10/10
10/15
10/15
Operation
Fertilizer
Pesticide
Harvest and kill
Tillage
Tillage
Planting
Fertilizer
Fertilizer
Type
N granule
harmony
Rate
40 lbs/ac N
0.5 oz/ac
Chisel
Disk
Rye/wheat
N granule
P2O5
20 lbs/ac N
50 lbs/ac P
139
Table A.4. Schedule of management operations for timothy under the baseline scenario
Date
4/15
4/15
6/15
6/20
8/15 (1st5th years)
Operation
Fertilizer
Fertilizer
Harvest
Fertilizer
Harvest
8/15
10/1
10/1
10/1
10/10
10/10
10/10
Harvest and kill

Tillage
Tillage
Tillage
Fertilizer
Fertilizer
Planting
Type
N granule
P2O5
Rate
60 lbs/ac N
13 lbs/ac P
N granule
50 lbs/ac N
Renew stand in 6th year

Moldboard
Disk
Hallow
N granule
P2O5
Timothy
60 lbs/ac N
45 lbs/ac P
Table A.5. Schedule of management operations for hay under the baseline scenario
Date
4/10
4/10
4/10
4/20
4/20
4/20
5/15
5/20
7/15
7/20
9/15 (1st5th years)
Operation
Fertilizer
Fertilizer
Fertilizer
Pesticide
Pesticide
Pesticide
Harvest
Fertilizer
Harvest
Fertilizer
Type
N granule
P2O5
K2O
2,4-D
Banvel
Sevin
Rate
40 lbs/ac N
13 lbs/ac P
25 lbs/ac K
1 qt/ac
1pt/ac
N granule
50 lbs/ac N
N granule
50 lbs/ac N
Harvest
9/15 (6th
year)
10/1
10/1
10/1
10/1
10/1
10/10
Harvest and kill

Tillage
Tillage
Tillage
Fertilizer
Fertilizer
Planting
Moldboard
Disk
Hallow
N granule
P2O5
Orchard grass mix with
wheat or rye nurse crop
140
50 lbs/ac N
45 lbs/ac P
Table A.6. Schedule of management operations for pasture under the baseline scenario
Date
4/15
4/15
4/15
4/20
4/20
4/20
Operation
Fertilizer
Fertilizer
Fertilizer
Pesticide
Pesticide
Pesticide
Type
N granule
P2O5
K2O
2,4-D
Banvel
Sevin
5/1
Grazing (May 1-Oct 31)
Manure
7/10
Fertilizer
11/1
11/5
11/5
11/5
11/10
N granule
Harvest and kill
Tillage
Moldboard
Tillage
Disk
Tillage
Harrow
Orchard grass mix
Planting
with wheat or rye
nurse crop
Rate
25 lbs/ac N
20 lbs/ac P
25 lbs/ac K
1 qt/ac
1 pt/ac
92.824 kg/ha/d cow
manure, 39.727
kg/ha/d horse manure
25 lbs/ac N
Table A.7. Schedule of management operations for lawns in urban lands (except transportation) under the baseline scenario
Date
3/20
3/20
4/15
5/1
5/1
5/1
5/15
6/1
6/12
6/12
6/15
7/1
7/15
7/24
7/24
8/1
8/15
9/1
9/14
9/14
9/15
10/1
10/16
10/16
10/20
Operation
Fertilizer
Fertilizer
Harvest
Fertilizer
Fertilizer
Harvest
Harvest
Harvest
Fertilizer
Fertilizer
Harvest
Harvest
Harvest
Fertilizer
Fertilizer
Harvest
Harvest
Harvest
Fertilizer
Fertilizer
Harvest
Harvest
Fertilizer
Fertilizer
Harvest
Type
N granule
P2O5
Rate
25 lbs/ac N
5 lb/ac P
N granule
P2O5
25 lbs/ac N
5 lb/ac P
N granule
P2O5
25 lbs/ac N
5 lb/ac P
N granule
P2O5
25 lbs/ac N
5 lb/ac P
N granule
P2O5
25 lbs/ac N
5 lb/ac P
N granule
P2O5
25 lbs/ac N
5 lb/ac P
141
Table A.8. Schedule of management operations for lawns in urban transportation lands under the baseline scenario
Date
5/1
6/1
7/1
8/1
9/1
10/1
Operation
Harvest
Harvest
Harvest
Harvest
Harvest
Harvest
Type
142
Rate

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Neshanic River Watershed Restoration Plan

SWAT Modeling Analysis for the Neshanic River Watershed

7.2.2. Sediment Yields and Source Assessment ............................................... 80

8. BMP Scenarios ........................................................................................................ 121

Management Schedules for Crops and Lawns .......................... 139

2. The Neshanic River Watershed

Figure 2.1. The Neshanic River watershed and study area

3. Water Quality Criteria

4. Pollutant Source Characterization

4.1. Point Sources

Fertilizer and manure application to croplands

4.2.1. Row Crop and Other Agricultural Lands

Manure pro- Fecal coliform in

4.2.4. Urban / Industrial Lands

4.2.5. Household Sewage Treatment Systems (HSTS)

Table 4.5. Estimated septic tanks and failures in Hunterdon County

Failure rate (%)

Figure 4.1. Septic system areas in the Neshanic River Watershed

SWt SW0 Rday Qsurf Ea Wseep Qqw i

Figure 5.1. Nitrogen Processes Modeled in SWAT (USDA-ARS, 1999).

Figure 5.2. Phosphorus Processes Modeled in SWAT (USDA-ARS, 1999).

5.2. Input Data

Figure 5.3. Elevation map of the Neshanic River Watershed

5.2.2. Soil Data

Figure 5.4. Soils of the Neshanic River Watershed

Table 5.1. Soils and area distributions

Readington silt loam, 6 to 12 percent slopes, eroded

5.2.3. Land Use Data

Figure 5.5. Land use of the Neshanic River Watershed

Table 5.2. Land uses and are distributions*

* 2002 land use data with 2007-2008 updates

5.2.4. Weather Data

Figure 5.6. Delineation of the Neshanic River Watershed

5.4. Baseline Scenario of Pollutant Sources and Management Practices

5.4.1.1. Agricultural Management Practices

Table 5.4. Designed HRUs with manure application

5.4.1.2. Cattle Direct Deposit

5.4.1.3. Wildlife Deposit

5.4.1.4. Urban Runoff

5.4.1.5. Failing Septic Systems

5.4.1.6. Groundwater Contamination

Minimum value for the cover and

S is the mean simulated value.

Wash-off fraction for persistent bacteria

5.5.3. Crop Yield Calibration

6. Calibration Results and Discussion

Annual Flow (m3/s)

Figure 6.1. Annual observed and simulated stream flows at Reaville

Monthly Flow (m3/s)

Figure 6.2. Monthly observed and simulated stream flows at Reaville

Mean relative error

* Switch the observed stream flows on September 16 and 17, 1999.

Daily Flow (m3/s)

* Switch the observed stream flows on September 16 and 17, 1999.

Mean relative error

* Switch the observed stream flows on September 16 and 17, 1999.

Daily flow (m3/s)

Percent of time that flow is equaled or exceeded

6.2. Sediment Calibration

Obserbed instanteneous flow

Observed daily flow

Simulated daily flow

Table 6.4. Statistics of TSS loading calibration and validation at Reaville

1997-2002 mean (19 days)