CSIRO PUBLISHING

Marine and Freshwater Research, 2010, 61, 936–949 www.publish.csiro.au/journals/mfr

Ecology and management of subsurface groundwater

dependent ecosystems in Australia ] a review

Moya TomlinsonA,B and Andrew J. BoultonA

A
Ecosystem Management, University of New England, Armidale, NSW 2351, Australia.
B
Corresponding author. Email: moyatomlins@gmail.com

Abstract. As demand for consumptive use of groundwater escalates, the need for careful management becomes more
pressing. Water reforms in Australia require explicit recognition of environmental needs in water resource plans, but
subsurface groundwater dependent ecosystems (SGDEs) are rarely provided for. The ecological values of these
sequestered ecosystems are not well documented and are readily overlooked. We review the biodiversity, ecological
processes and ecosystem services of Australian SGDEs and highlight the ecological relevance of their connectivity with
other ecosystems. A lack of attention to SGDEs in groundwater plans risks inadequate provision for environmental water
requirements with probable impacts on ecological values, water quality and ecosystem goods and services in SGDEs and
connected ecosystems. We suggest an ecohydrogeological approach to understanding the implications of anthropogenic
disturbance on SGDEs based on their connectivity to other ecosystems and aquifer permeability. As well as a template for
comparative research on the biogeochemistry and ecology of SGDEs in Australia and overseas, this conceptual tool has
potential application in conservation planning, water resource assessment and environmental impact assessment.

Additional keywords: aquatic conservation, aquifer permeability, ecohydrogeology, environmental water requirements,
groundwater regime, stygofauna, water resources.

Introduction vegetation and surface aquatic communities; Land and Water

As demand for groundwater increases, so does the imperative
for better groundwater management (Danielopol et al. 2003;
Humphreys 2006). Growing awareness that aquifers are dynamic
ecosystems rather than simply underground water storages has
prompted questions from resource managers on how to identify
and provide for the environmental values of groundwater.
Aquatic ecologists have focussed on surface water ecosystems,
largely leaving groundwater research and management to
hydrogeologists, although the tide is turning (e.g. a 2009 special
issue of the Hydrogeological Journal focussed on integrating
ecology and hydrogeology). A review is timely because the lit-
erature on the ecology of subsurface groundwater dependent
ecosystems (SGDEs) is broad, poorly integrated and seldom
readily available to hydrogeologists or managers. We define an
SGDE as ‘an aquatic ecosystem occurring below the surface of
the ground that would be significantly altered by a change in the
chemistry, volume and/or temporal distribution of its ground-
water supply’ (adapted from Parsons and Wentzel 2007).
Australia’s national water reforms require an environmental
provision in water plans (Commonwealth of Australia 2004).
However, environmental ‘flow’ setting for groundwater has
received scant attention, although it is understood to involve
identifying groundwater dependent ecosystems (GDEs) and
assessing the nature of their groundwater dependency (SKM
2001). Some progress has been made with identification and
assessment of surface GDEs (e.g. groundwater dependent
Australia 2009), but subsurface GDEs are routinely ignored in
ecological assessments for management, particularly in water
planning, but also in conservation planning and environmental
impact assessment. This risks inadequate protection of environ-
mental goods and services, which underpin the health and
productivity of SGDEs and connected ecosystems.
Here, we review the scattered literature on biodiversity and
ecological processes in Australian SGDEs and list their ecosys-
tem services. To facilitate research and management of SGDEs,
we propose an ecohydrological approach to understanding
anthropogenic disturbance based on the connectivity of SGDEs
to other ecosystems and aquifer permeability. We conclude with
research gaps evident from our review, emphasising those that
must be filled urgently to support wise management of this finite
resource in Australia. Many of these research gaps also exist
overseas and our review has relevance for SGDEs worldwide.
Groundwater biodiversity in Australia
Australian SGDEs harbour surprising biodiversity (Humphreys
2008) of specialised groundwater fauna (stygobites sensu Gibert
et al. 1994) (Table 1). The groundwater environments are listed
in Table 1 as reported in the literature, but are not mutually
exclusive; for example, calcrete aquifers may or may not be
karstified, and calcrete deposits are often interdigitated with
alluvium, resulting in heterogeneous environments. Overall,

Ó CSIRO 2010 10.1071/MF09267 1323-1650/10/080936

Subsurface groundwater dependent ecosystems Marine and Freshwater Research 937

Table 1. Stygobitic biodiversity in Australia (Poore and Humphreys 1998; Humphreys 2000, 2001, 2006; Jaume et al. 2001; Thurgate et al. 2001;
Eberhard et al. 2005; Pinder et al. 2006)
Ticks indicate a record for the taxon

Taxa Calcrete Alluvial Anchialine Karst: freshwater Fractured rock

Protista ü
Platyhelminthes Turbellaria ü ü ü
Aschelminthes Nematoda ü
Rotatoria
Tardigrada ü
Annelida Oligochaeta ü ü ü ü
Polychaeta ü
Mollusca Gastropoda Hydrobiidae ü ü ü
Glacidorbidae ü
Arachnida Acarina ü ü
Crustacea Ostracoda Myodocopida ü
Podocopida ü ü ü
Halocyprida ü
Unidentified ü ü ü ü ü
Copepoda Cyclopoida ü ü ü
Harpacticoida ü ü ü
Calanoida ü ü
Misophrioida ü
Remipedia Nectiopoda ü
Syncarida Psammaspididae ü ü
Koonungidae ü ü
Anaspidae ü
Bathynellidae ü ü ü
Parabathynellidae ü ü ü ü ü
Undescribed family ü
Decapoda Atyidae ü ü ü ü
Isopoda Phreatoicidae ü ü ü ü
Janiridae ü
Flabellifera ü
Tainisopidea ü ü ü
Amphisopidae ü
Oniscidea ü
Cirolanidae ü ü
Amphipoda Paramelitidae ü ü
Neoniphargidae ü
Melitidae ü ü
Bogidiellidae ü
Hadziidae ü
Crangonyctidae ü ü
Chiltoniidae ü ü
Spelaeogriphacea ü
Thermosbaenacea ü ü ü
Insecta Coleoptera Dytiscidae ü ü
Elmidae ü
Vertebrata Pisces ü ü

diversity at the order and family is lowest in fractured rock
aquifers (Table 1), but this may be partly a result of uneven
sampling intensity across the different aquifer types.
Survey effort in Australia is patchy and incomplete, but
rapidly improving with many exploratory baseline surveys
being conducted, particularly in Western Australia as part of
the environmental impact assessment for mining developments
(Humphreys 2008; Eberhard et al. 2009; Hancock and Boulton
2009). Existing survey work covers some coastal and inland
alluvial, fractured rock and arid-zone karstic and calcrete
aquifers and caves. In Europe, the number of endemic stygofauna
(groundwater invertebrates) is greater in karstic systems than in
alluvial aquifers, perhaps because the greater isolation of karstic
habitats facilitates speciation (Danielopol et al. 2000). As eastern
Australian karst has only been sparsely surveyed (Thurgate et al.
2001), it is likely that much stygobitic diversity remains un-
documented. Furthermore, a great deal of information is not
readily accessible because it is in unpublished consultancy or
government reports or in individual researcher’s records. Apparent
patterns of biodiversity reflect sampling effort and available
938 Marine and Freshwater Research
taxonomic interest and expertise (Eberhard et al. 2009); un-
explored groups may be equally diverse.
As in Europe (Deharveng et al. 2009), crustaceans including
isopods, copepods, ostracods and amphipods dominate the
Australian stygofauna. For example, surveys to date have
revealed a new genus of isopod (Wilson 2003), over 110 species
of ostracod (Reeves et al. 2007) in the Pilbara region alone
(Fig. 1), and 31 species of copepod from the Murchison region,
part of the Yilgarn Craton (Karanovic 2004). Amphipods are
widespread and exhibit cryptic diversity and a high degree of
endemism (Cooper et al. 2007; Finston et al. 2007; Bradford
et al. 2010). Of the crustacean superorder Syncarida, anaspids
are restricted to southern Australia (Hobbs 2000). The bath-
ynellids are well represented and largely undescribed, although
the Western Australian fauna has received some attention (e.g.
Cho et al. 2005, 2006; Guzik et al. 2008). A wide range of other
taxa is represented in Australia, including over 90 new species of
stygobitic dytiscid diving beetles (Watts and Humphreys 2006;
Watts et al. 2007) and two species of fish (Humphreys 1999).
The diversity of subsurface microbial, fungal and protozoan
communities is virtually unexplored in Australia. However,
some biochemically novel, chemoautotrophic communities
consisting of mucoid sheets and dependent on nitrite oxidation
have been described from karst of the Nullarbor Plain (Fig. 1;
Holmes et al. 2001).
Patterns of subterranean faunal biodiversity are the product
of four characteristics (Gibert and Deharveng 2002): low
number of lineages owing to the ecological filter of the transition
to lightless environments; high endemism owing to habitat
fragmentation; high level of relict taxa owing to persistence of
subsurface refugia over long periods of unfavourable surface
Fortescue
valley Kimberley
Pilbara
Cape
Range
Murchison
region
Swan Nullarbor Plain
Coastal
Yilgarn
Plain
Perth
Leeuwin-Naturaliste
ridge
1000 km
Fig. 1. Outline map of Australia showing the locations mentioned in the text.
M. Tomlinson and A. J. Boulton
conditions (e.g. aridity); and truncated food webs with no
primary producers. Characteristic of the Australian stygofauna
are taxa that are relicts of ancient lineages and have very limited
distributions. The anchialine fauna of Cape Range (Fig. 1) is an
example of the persistence of phyletic relictual fauna hypothe-
sised to derive from populations already inhabiting subterranean
habitats before the break-up of Gondwana (Humphreys 2000).
This distinctive fauna includes the only southern hemisphere
representatives of the copepod order Misophrioida (Jaume et al.
2001), another crustacean order Thermosbaenacea (Poore and
Humphreys 1992) and the class Remipedia (Lasionectes exleyi
(Yager and Humphreys 1996), known from a single water-filled
cave at Cape Range). The only Australian records of the
peracarid crustacean order Spelaeogriphacea are two species
(of four globally) from the Fortescue valley in the Pilbara
(Fig. 1; Poore and Humphreys 1998, 2003).
Harvey (2002) defined short-range endemic species as those
with a range of less than 10 000 km2, and noted that most short-
range endemic species possess characteristics such as limited
dispersal ability and confinement to discontinuous habitats.
Eberhard et al. (2009) suggest that 1000 km2 may be a more
satisfactory threshold for short-range endemism of stygobites.
The high diversity of short-range endemic dytiscid diving
beetles in calcrete aquifers in the Pilbara (Watts and Humphreys
2006) has been attributed to multiple independent colonisations
of aquifers that subsequently became subterranean ‘islands’
isolated by the onset of aridity (Cooper et al. 2002; Leys et al.
2003). Studies of the mitochondrial DNA of amphipods (Cooper
et al. 2007; Bradford et al. 2010), oniscidean isopods (Cooper
et al. 2008) and parabathynellids (Guzik et al. 2008) from these
calcretes support this interpretation.
Great Artesian Basin
Tamworth
Subsurface groundwater dependent ecosystems
Terrestrial Riparian
vegetation vegetation
Vadose
Freshwater
zone
psammo-
littoral
SGDEs
Marine
Hyporheic
psammo-
zone
littoral
Marine
Marine and upwelling Surface
estuarine and intrusion waters
(Springs, rivers,
wetlands)
Fig. 2. Subsurface groundwater dependent ecosystems (centre) are linked
through ecotones (speckled area) to other ecosystems (outer circle).
Life-history adaptations by stygofauna to the relatively more
stable aquifer environment include fewer but larger eggs,
prolonged egg development (Rouch and Danielopol 1999) and
greater longevity compared with phyletically related surface-
dwelling taxa (Dole-Olivier et al. 2000). These data are all from
studies of European fauna. Although equivalent physiological
adaptations and life histories may be assumed for Australian
stygofauna, research is needed to confirm this assumption.
These life-history adaptations to the relatively stable aquifer
environment would not be advantageous in a situation of rapid
environmental change such as anthropogenic water level fluc-
tuations. Diapause in unfavourable environmental conditions
is known for surface-water species of taxa with groundwater
representatives (e.g. copepods; Hairston and Caceres 1996),
but has not yet been recorded in groundwater forms. Fauna in
unconfined aquifers are potentially vulnerable to stranding if
the amplitude and frequency of watertable fluctuations are
increased by groundwater extraction. Microcosm experiments
on stygofauna from bores near Tamworth, NSW (Fig. 1),
indicate that small-bodied fauna such as copepods are able
to follow declining water levels, but larger animals such as
amphipods become stranded (Tomlinson 2009).
Habitat diversity in the subsurface
Widespread perceptions of reduced habitat heterogeneity,
low productivity and unfavourable environmental conditions
(e.g. low dissolved oxygen, high sulfur) belie the true diversity
of aquifer habitats and the habitat differences that are key to
appreciating the subtle complexities of subterranean ecology.
Despite the shared characteristics of being subterranean and
lightless, karstic, calcrete, alluvial, fractured rock and other
groundwater environments differ in many ecologically relevant
features. For example, subsurface environmental conditions
may exhibit steep gradients in physico-chemical conditions, and
Marine and Freshwater Research 939
Humphreys et al. (2009) conceptualise Western Shield calcretes
as ‘groundwater estuaries of salt lakes’ owing to their analogous
environmental heterogeneity. This illustrates the main problem
facing efforts to classify subsurface habitats – continua exist at
multiple spatial scales and habitat types grade into each other.
Furthermore, each aquifer type is unlikely to be a discrete
habitat harbouring a distinctive fauna. In some environments,
such as calcretes and mound springs, short-range endemism is
high, yet where connections between habitats exist there may be a
broad overlap of taxa, although richness and abundances differ.
Except for large-bodied taxa such as fish that require large
voids, stygofauna from the Pilbara and adjacent areas are found
wherever groundwater environments provide suitable habitat
(Eberhard et al. 2005), including in porous, karstic and frac-
tured-rock aquifers as well as in the hyporheic zone and springs.
The tendency to habitat generality by many taxa indicates that
conclusions about habitat affinity and consequent faunal distribu-
tion based on limited sampling should be drawn with caution.
Nevertheless, consideration of habitat helps to assess the like-
lihood that subterranean fauna may occur in a water-planning area
or the potential zone of impact of a mining development. Habitat
characteristics also govern the best sampling design and method
to assess the distribution and diversity of subterranean faunal
communities (Eberhard et al. 2009). The degree of connectivity to
other likely habitats is crucial because it affects recolonisation
sources and pathways, the potential for endemism, and the
magnitude and type of repercussions for other ecosystems.
Subsurface groundwater dependent ecosystems are often
hydrologically and ecologically connected to terrestrial and
aquatic surface ecosystems through transition zones including
the hyporheic zone, the vadose zone, marine upwelling and
intrusion zones, and the psammolittoral zone (Fig. 2). There may
also be direct connections between SGDEs, for example, where
an alluvial aquifer overlies or interdigitates with another aquifer
type such as calcrete or fractured rock (Eberhard et al. 2009).
The interfaces between habitats are usually characterised by
spatially and temporally dynamic gradients in environmental
conditions that defy precise delineation of ecosystem bound-
aries. These ‘dynamic ecotones’ (Vervier et al. 1992) are zones
of exchange of materials and energy and potential pathways for
faunal dispersal and transmission of contaminants.
The hyporheic zone is the saturated sediments below and
alongside stream beds where surface water and groundwater
mix (White 1993). In the arid zone, the hyporheic fauna of
ephemeral streams is groundwater dependent most of the time,
with many species relying entirely on subsurface water after
surface pools have dried (Boulton et al. 1992; Cooling and
Boulton 1993). Where rainfall is low and groundwater tables
support terrestrial vegetation (O’Grady et al. 2009), fauna in the
vadose zone can be considered groundwater dependent because
vadose zone moisture is discharging groundwater. In karstic
aquifers, the vadose zone is a complex rock–soil interface
termed epikarst (i.e. ‘skin of karst’; Bakalowicz 2004). The
epikarst in Europe (Pipan and Culver 2007) and North America
(Pipan et al. 2006) harbours a diverse stygofauna distinct
from the fauna found in the saturated zone. This habitat has
been sparsely sampled in Australia, but stygofauna have been
recorded in the vadose infiltration waters of karstic caves in
south-western Western Australia (Eberhard 2004).
940 Marine and Freshwater Research M. Tomlinson and A. J. Boulton
Although not exclusive to groundwater environments, in combination these characteristics form a suite of powerful drivers of faunal biodiversity, predominant subsurface ecological processes and the

Some species are able to respond rapidly to prolonged increases in food availability.
The interconnections between SGDEs and surface aquatic

A low number of lineages have passed through the ecological filter of lightlessness.
Microbes rather than plants are the basis of the food chain and therefore have key
that taxonomic approaches combine morphological and molecular investigations.
in groundwater regime. Morphological similarity and cryptic speciation requires systems are best known in alluvial aquifers that hydraulically
Persistent habitat for relict lineages. Fauna are potentially vulnerable to changes

Some species have restricted ability to respond rapidly to environmental change

High potential for speciation and short range endemism. Vulnerable to habitat
interact with rivers and floodplains. In these environments, the

or to recolonise readily after local extinction; low resilience and resistance.

Implications for biodiversity, ecological processes and ecosystem services

hyporheic zone often extends not only longitudinally along the

Close monitoring is required to detect population decline, but response

river, but also laterally (potentially for kilometres). Stanford and
Ward (1993) proposed that alluvial aquifers are a component of a
continuum in which the aquifer–river complex can be concep-
tualised as a network of active channels and a series of hydro-
geological units linked dynamically by the ‘hyporheic corridor’.
roles in supporting biodiversity and ecosystem function.

change resulting in local or total extinction of species.

On a larger scale, alluvial aquifers represent an interstitial high-
way linking spatially discontinuous subterranean ecosystems
with surface waters (Ward and Palmer 1994). We know little
Table 2. Characteristics of groundwater environments and implications for groundwater biodiversity and ecology

of the potential effects on stygofauna and groundwater processes

of anthropogenic disruptions of this subsurface connectivity, and
this is a major research gap in Australia and overseas. Progress is
further hampered by practical constraints on obtaining quantita-
tive faunal samples from the hyporheic zone, although this is an
active field of research (e.g. Kibichii et al. 2009).
ecosystem services provided by subsurface groundwater dependent ecosystems

time can be decades.

Ecological processes in groundwater environments

As most subterranean food webs are heterotrophic (Table 2), they
rely on water percolating through the vadose zone or exchanging
across the hyporheic zone to supply organic matter and dissolved
oxygen. The transfer of carbon from particulate and dissolved
organic matter to invertebrates is mediated by biofilms coating
No primary producers; herbivores represented only by root-mat feeders;

sediment particles and rock surfaces (Bärlocher and Murdoch

Fauna have slower metabolic rates (Danielopol et al. 1994), longer life
fewer predators; a trophic shift towards omnivory; food web truncated
Fauna are morphologically conservative. Selective pressure towards

1989). Biofilms transduce nutrients and energy (Battin et al.

cycles and lower fecundity (Dole-Olivier et al. 2000) than surface
Buffering from environmental change taking place at the surface.

delayed breeding, longer life cycles, larger size and fewer young.

2003) through processes including abiotic adsorption of mole-

cules to the biofilm matrix and biological uptake by enzymatic
counterparts. Overall densities are usually very low owing to
and dominated by detritivores (Gibert and Deharveng 2002).

hydrolysis. The spatial availability of electron acceptors is

determined by patterns of water flow, which in turn are driven by
hydrologic connectivity and hydraulic conductivity (Baker et al.
2000a; Kasahara et al. 2009). Under aerobic conditions, oxygen
acts as an electron acceptor, but under anaerobic conditions other
Reduced habitat heterogeneity (Sket 1999).

compounds are acceptors in a reduction sequence of nitrate,

manganese, iron, sulfate and carbon dioxide (Wetzel 2001).
Restricted dispersal and recruitment

Microbial activity is typically highest near the source of recharge

and gradually declines with distance (Kaplan and Newbold
2000). In aquifers connected to surface waters, the hyporheic
zone is a crucial interface for fluxes of nutrients (Boulton et al.
Implications for fauna

1998; Fischer et al. 2005), but other sources of recharge can be

significant. For example, flood pulse inundation in a semiarid
catchment in New Mexico altered rates of nutrient retention
lack of food.

and organic matter processing in floodplain groundwater (Baker

et al. 2000b). Local lateral exchange processes such as cycles
of bank discharge and recharge may also govern the timing
and direction of nutrient processing in floodplain groundwater
Typically restricted inputs of energy;

(Lamontagne et al. 2005b).

The functional diversity of subsurface ecological processes
Relatively stable environmental

is determined by dynamic gradients in oxygen, nutrients and

surface aquatic environments
groundwater environments

physico-chemical conditions. The co-occurrence over small

conditions compared with

May be spatially discrete

spatial scales (o10 mm) of coupled processes (e.g. nitrification

and denitrification) contributes to the characteristic patchiness
Characteristics of

low productivity

of SGDEs. In unconfined alluvial aquifers with fluctuating

water tables, a significant portion of organic carbon metabolism
or patchy

may occur in oxic–anoxic cycles in the zone of intermittent

Lightless

saturation (Vinson et al. 2007). This zone may be functionally

analogous to the hyporheic zone of intermittent streams where
Subsurface groundwater dependent ecosystems Marine and Freshwater Research 941

episodic wetting events stimulate biogeochemical ‘hot
moments’ of elevated reaction rates (McClain et al. 2003).
Interstitial storage of dissolved organic matter and the avail-
ability of dissolved oxygen are influenced by particle size and
pore size (Maridet et al. 1996). Larger particle size and high
porosity allows higher flows and higher availability of oxygen,
but reduces entrapment and retention of nutrients. In fractured
rock and karstic aquifers, uneven porosity resulting from the
distribution of fissures, fractures and solution pipes creates
preferential flow paths that generate spatial heterogeneity in
biogeochemical cycling (Ayraud et al. 2006). Spatial and
temporal variability in groundwater flow paths is also influ-
enced by surface microtopography (Pfeiffer et al. 2006) and by
stream channel morphology (Dahm et al. 1998).
As in other ecosystems, heterogeneity in subsurface envir-
onments is a major determinant of ecosystem function (McCarty
et al. 2007). Disturbances such as disruption to patterns of
hydrological connectivity (Baker et al. 2000b) and sediment
wetting–drying cycles (Baldwin and Mitchell 2000) potentially
alter spatial and temporal patterns of groundwater flow, flux and
quality, with implications for rates of organic matter miner-
alisation and nutrient cycling. For example, pumping from a
fractured rock aquifer in north-west France disturbed water flux
in the aquifer, reduced groundwater residence time and drasti-
cally modified the water chemistry, slowing many biogeochem-
ical processes (Ayraud et al. 2006). Prolonged desiccation of
sediments caused by water table drawdown is likely to alter the
balance between aerobic and anaerobic processes and change
the composition of microbial populations, reducing the inci-
dence or rate of anaerobic metabolism. Disturbance to the
groundwater regime may change the rate and nature of sub-
surface ecological processes, resulting in reduced availability
of carbon, nitrogen and phosphorus, with flow-on effects for
biodiversity and ecosystem services not only within the SGDE,
but also in connected surface ecosystems such as rivers, riparian
zones and estuaries. Understanding the mechanisms and impli-
cations of these changes to the groundwater regime remains one
of the most significant research gaps in groundwater science
worldwide, and severely hampers effective management of this
increasingly used resource.
Ecosystem goods and services
Ecosystem goods and services are the conditions and processes
whereby natural ecosystems and their component species sustain
and fulfil human life (Daily et al. 1997). Goods are tangible,
direct benefits. Services are ecological functions that benefit
humans. Although goods can readily be assigned a value, services
are less tangible and far more difficult to value. As surface waters
deteriorate in quality and quantity and demands on groundwater
increase, there is a risk that the demands for consumptive use of
groundwater will prioritise the use of ecosystem goods over the
maintenance of ecosystem services. The use of groundwater may
continue in excess of recharge for some time before the impacts
of extraction on ecosystem services become apparent.
Groundwater ecosystem goods and services span four main
types (Table 3). Provisioning services (goods) are of obvious
value, but the less familiar supporting, regulating and cultural
services are also significant. Bioremediation of contaminants
such as chlorinated solvents, polycyclic aromatic hydrocarbons
(Bamforth and Singleton 2005) and volatile aromatics occurs
both aerobically and anaerobically (Andreoni and Gianfreda
2007), often at the edge of contaminant plumes where electron
donors (e.g. hydrogen) from the plume mix with electron
acceptors from the surrounding groundwater across a steep
physico-chemical gradient (Bauer et al. 2009). The rate of
groundwater flow is critical to effective bioremediation; faster
flow reduces interactions between water, the matrix and its
biofilm, thus limiting the potential for contaminant removal or
attenuation (Malard et al. 1997), but low flows may facilitate
clogging (Mauclaire et al. 2006). The role of other aquifer biota
in bioremediation is poorly understood, although protozoan
grazing promotes biodegradation by stimulating bacterial activ-
ity (Mattison et al. 2005), and a similar role seems likely for
stygofauna. For example, stygofaunal crustaceans were impli-
cated in the remediation of groundwater contaminated by
bacteria from an effluent disposal area on the Canterbury Plains,
South Island, New Zealand (Sinton 1984; Boulton et al. 2008).
In Australia, we have no data on the potential for endemic
stygofauna as bioremediation agents.
Biogeochemical processes in alluvial aquifers, such as the
breakdown of organic matter, attenuation of high nitrogen inputs
from anthropogenic sources and delivery of nutrients to streams
via groundwater discharge, contribute to surface GDEs such as
riparian, floodplain and instream vegetation (Baker et al. 2000b;
Hayashi and Rosenberry 2002). Many groundwater hetero-
trophic bacteria reduce nitrate and play key roles in the miner-
alisation of organic matter and other biogeochemical processes
(Baldwin and Mitchell 2000; Mermillod-Blondin et al. 2005).
Bacterial activity may affect the physical and hydraulic proper-
ties of aquifers through the production or dissolution of inter-
granular cements (Chapelle 2000).

Table 3. The main categories of ecosystem services (Millennium Ecosystem Assessment 2005) provided by groundwater

Type of service Examples

Provisioning Water for drinking, irrigation, stock and industrial use. Approximately 20% of total consumptive water use
in Australia is from groundwater (Commonwealth of Australia 2007).
Supporting Bioremediation: the process, either spontaneous or managed, of degradation or transformation of contaminants
by living organisms, mostly bacteria, into non-toxic or less toxic products (Chapelle 2000); ecosystem engineering;
nutrient cycling; denitrification; water-quality indicators; support to linked ecosystems;
refugia for fauna from linked ecosystems.
Regulating Aquifers mitigate flooding and erosion by absorbing and storing run-off. They supply surface ecosystems.
Cultural Indigenous spiritual values, scientific values, cave tourism.
942 Marine and Freshwater Research
Groundwater discharge contributes to river flow (Wood
et al. 2005; Cook et al. 2006), supports instream and riparian
communities (Boulton and Hancock 2006), wetlands (McCarthy
2006), and aquatic communities in caves (Eberhard 2004),
springs and springbrooks (Meyer et al. 2003), sustains terrestrial
vegetation (Lamontagne et al. 2005a; O’Grady et al. 2009)
and supports some estuarine and marine ecosystems (Linderfelt
and Turner 2001; Dale and Miller 2007). Grazing of biofilms
by stygofauna is postulated to prevent overgrowth of biofilm
and consequent sediment clogging, as demonstrated for a soil
flagellate by Mattison et al. (2002). Benthic and hyporheic fauna
achieve similar outcomes through mechanical bioturbation and
pelletisation (e.g. Mermillod-Blondin et al. 2003; Nogaro et al.
2006), thereby contributing to a sustainable water supply for a
range of consumptive and non-consumptive uses.
Some surface aquatic taxa resist water loss and desiccation
by migration into moist or saturated refugia including SGDEs
(Boulton et al. 1992; Harris et al. 2002). Fish in floodplains
of the east Kimberley retreat to karst sinkholes during the dry
season (Humphreys 1995). Groundwater discharge into estu-
aries may provide refuge zones for salt-sensitive species during
periods of hypersaline conditions associated with reduced river
discharge during droughts (Taylor et al. 2006). On an evolu-
tionary scale, aquifers have provided refugia from changing
environmental conditions on the surface, including the onset of
aridity in Australia (Cooper et al. 2002; Finston et al. 2007).
Subsurface groundwater dependent ecosystems provide
crucial regulating services such as flood control and erosion
prevention. Aquifer storage of run-off and stream flow is
particularly significant in zones of strong groundwater–surface
water connections such as river banks and floodplains (Brunke
and Gonser 1997; Sophocleous 2002). This ‘buffering effect’
reduces the flashiness of stream discharge, with important
hydrological repercussions for surface fauna and processes
(Bunn and Arthington 2002).
Groundwater has strong cultural values in Indigenous Aus-
tralia. Stories associated with groundwater-related sites such as
springs, mound springs, caves and native wells played a role
in traditional law and protocols (Moggridge 2007). In the arid
zone, groundwater in streambeds supplies drinking water and
supports important ‘bush tucker’ such as the plant Ipomoea sp.
listed under the Commonwealth Environment Protection and
Biodiversity Conservation Act (Department of the Environment
Water Heritage and the Arts 2008). The Indigenous relationship
with aquatic systems may be understood as a socio-ecological
relationship equivalent to kinship relations of obligation and
care (Jackson 2006), suggesting that contemporary Aboriginal
communities have cultural reasons for involvement in ground-
water management.
Stygofauna are potential indicators of ecosystem condition
and the integrity of fundamental ecological processes in ground-
waters. Despite pleas for ecosystem-level management (e.g.
Likens et al. 2009), current river health assessment in Australia
does not consider the condition of hyporheic zones (Boulton
2000; Hancock 2002) or connected alluvial aquifers. Inclusion
of these components would enhance the robustness of river
health assessment (Reid and Brooks 2000), especially in ephe-
meral arid zone rivers with subsurface flow. In aquifers, the
relative abundance of surface water and groundwater taxa can be
M. Tomlinson and A. J. Boulton
related to the flow patterns of pollutants (Malard et al. 1994,
1996) and to aquifer hydrodynamics (Dumas et al. 2001).
A dominance of stygobites indicates low surface water inputs,
and may indicate the absence of nitrate-enriched surface water
in aquifers (Claret et al. 1999).
If stygofauna are more sensitive than surface water fauna to
chemical pollutants (Plénet 1999; Mosslacher 2000), ground-
water quality criteria based on the responses of surface water
organisms may be insufficient to protect groundwater systems
(Hose 2005). The use of stygofauna as biomonitors of heavy
metal contamination has been explored in Europe (e.g. Plénet
et al. 1996; Canivet and Gibert 2002), but there is no equivalent
work in Australia.
Consideration of scale in SGDE management
Only in the past decade have Australian groundwater managers
become aware of ecological considerations such as the water
needs of GDEs and the maintenance of groundwater ecosystem
function (Tomlinson and Boulton 2008). Groundwater man-
agement must be across ecologically relevant scales because
these environments are dynamic ‘open’ systems where biolo-
gical and geochemical interactions and transformations occur
at a range of scales. At a broad scale (103 m), resource avail-
ability in the subsurface is determined by aquifer type; geology
largely determines the porosity and contributes to the hydraulic
conductivity of the aquifer matrix. This affects the rate of
groundwater recharge as well as ecological aspects such as the
available physical living space for fauna, the entrainment of
organic matter and the supply of nutrients and dissolved oxygen
(e.g. Ward et al. 1994; Rouch and Danielopol 1999).
On finer scales (10 3 m), exchange processes between
surface and groundwater are ecologically relevant (Sophocleous
2002). These are often patchy, where zones of higher trans-
missivity (e.g. downwelling zones in stream channels) can
promote the supply of organic material that is the basis of
many subsurface food webs (Datry et al. 2005; Hancock et al.
2005) to create ‘hot spots’ of biodiversity and/or activity.
Fine-scale spatial variability in biogeochemical processes
and faunal distribution, abundance and richness coupled with
shifting physico-chemical gradients create a rich mosaic of
microenvironments (Pospisil 1994; Coineau 2000), constitut-
ing a set of functional mesohabitats that may be distinguished
by hydraulic and physical characteristics (Brunke et al. 2001;
Kasahara et al. 2009). These characteristics are likely to be
hierarchically scaled, rather like a series of filters controlling
faunal distribution (Poff 1997). For example, Reeves et al.
(2007) found that subregional differentiation in ostracod
genera in the Pilbara, Western Australia, was determined
primarily by altitude, then surface drainage basin, and finally
aquifer. Conversely, stygofaunal composition within an allu-
vial aquifer near Perth, Western Australia (Fig. 1), did not
match geological, chemical or topographical features, but was
better characterised by finer-scale abiotic conditions, includ-
ing dissolved oxygen and temperature (Schmidt et al. 2007).
Danielopol et al. (2004) urged the European Union Ground-
water Directive to account for the different vulnerabilities of
alluvial sediments and karstic systems, and this broad division
of aquifer types was the basis for an assessment of groundwater
Subsurface groundwater dependent ecosystems
biodiversity across six European regions (Dole-Olivier et al.
2009). Meanwhile, in response to the management requirements
of the EU Water Framework Directive, Dahl et al. (2007)
proposed a multi-scale typology of groundwater–surface water
interactions based on geomorphic, geological and hydrological
concepts reflecting functional linkages and controlling flow
processes at reducing scales. On a catchment scale (flow paths
45 km) groundwater flow was classified by regional geomor-
phology; on an intermediate or reach scale (1–5 km) ground-
water–riparian interactions were classified by hydrogeology; and
at a local scale of 10–1000 m classification was based on flow
path distribution. Flow regime delineates groundwater bodies and
illustrates their vulnerability to pollution. Vulnerability assess-
ment involves considering the travel time of infiltrating water, the
effectiveness of the hydrological connection between surface and
groundwater, and the hydrogeological attributes of the aquifer
materials (Quevauviller 2008).
Hahn and Fuchs (2009) applied a scale-based, ecologically
focussed hierarchical typology approach to the identification
of groundwater habitats in the south-western German state of
Baden-Württemberg (37 750 km2). The state was separated into
regional geological units that were subdivided into geohydro-
logical groups (aquifer types). The stygofaunal community
structure broadly matched the geohydrological groups, and
was more finely associated with subtypes characterised by
differences in porosity and hydraulic conductivity, which influ-
enced the hydrological exchange and amount of living space.
Is a typology of SGDEs needed?
Classification of potential habitats in SGDEs may help predict
stygofaunal biodiversity, abundance, distributions and com-
munity structure and would therefore be useful in determining
priorities for surveys and management applications, such as
assessing vulnerability to risks and identifying conservation
priorities (Castellarini et al. 2007a, 2007b). However, few
habitats are delineated by discrete boundaries, and the cate-
gories in any typology are defined for a particular purpose and
reflect hypotheses about relevant organising principles. The
dividing lines therefore differ according to the intended appli-
cation, and in every case are fuzzy in space and time. A typology
used as a fixed classification for all applications will be mis-
leading, but when applied as a heuristic tool (e.g. Hahn 2009)
may offer insights and guidance to management decisions. This
cautionary note is particularly pertinent for the management of
aquatic ecosystems owing to their inherently high connectivity
(Nel et al. 2009). Any categorisation of SGDEs in Australia,
although based on an initial identification of broad aquifer types
(e.g. karstic, fractured rock, alluvial), must then consider the
range and variability in climatic conditions across the continent
(Stern et al. 2000) because these will determine patterns of
recharge and discharge, strong drivers of spatial and temporal
differences in groundwater regime and subsurface resource
supply, particularly where connectivity to the surface is high.
Degrees of porosity determine available living space for fauna
and biofilms, place physical constraints on faunal size and
food particles (e.g. particulate organic matter) and affect
hydraulic conductivity and therefore the delivery rate of oxygen,
particulate organic matter and solutes. On a finer scale, localised
Marine and Freshwater Research 943
heterogeneity in substrate characteristics produces gradients or
patchiness in the availability of habitat and food.
Thus, we argue that the most effective typology of SGDEs
will be based on ecohydrogeological principles relating aquifer
characteristics (e.g. porosity and permeability), groundwater
regime and connectivity across aquifers and to adjacent ecosys-
tems, and will be arranged in a tiered hierarchy that acknow-
ledges how the broad-scale ‘filters’ (sensu Poff 1997) of climate,
surface drainage and recharge, geology and topography will
govern finer-scale aspects such as porosity and groundwater
flow. In turn, these broad-scale and fine-scale aspects determine
ecological processes and habitat availability, influence produc-
tivity and stygobite diversity, and control the provision of
groundwater ecosystem goods and services, as reviewed above.
Research is now needed on how these aspects and filters interact
in different SGDEs worldwide, and how aquifer characteristics,
groundwater regime and hydrological connectivity affect eco-
logical features and water quality in SGDEs.
Using an ecohydrogeological approach in management
Guiding conservation planning
Some Australian subterranean species and several groundwater
dependent communities are listed under biodiversity protection
legislation, but this mechanism is necessarily only applicable to
species and communities under a demonstrable and significant
threat (e.g. the root-mat communities in the karstic caves in the
Swan Coastal Plain and the Leeuwin-Naturaliste Ridge, Fig. 1;
Jasinska et al. 1996). More comprehensive and precautionary
biodiversity protection is potentially afforded through pro-
tected area systems. Planning for reserve networks relies on
habitat classification schemes such as those developed to
implement the Ramsar Convention (Ramsar Convention on
Wetlands 1971), but this wetland classification subsumes all
subterranean wetlands under the category ‘Karst and other
subterranean hydrological systems, inland’, effectively blur-
ring the distinctions between habitat types. The classification
used by the Directory of Important Wetlands in Australia nar-
rows this category to ‘Inland, subterranean karst wetlands’
(Environment Australia 2001). Work is underway to develop
an Australian National Aquatic Ecosystem classification which
will include a broader range of attributes and allow recognition
of the diversity of SGDEs.
Although some subterranean wetlands are serendipitously
included in the existing protected areas systems, most occur in
areas of high and competing demands for water and mineral
resources. The creation of a national park based on subterranean
ecological values seems unlikely in Australia for any but
spectacular cave ecosystems. However, a precedent exists
in Europe with the designation in 1996 of the Alluvial
Zone National Park, protecting the alluvial landscape in a free-
flowing section of the Danube River downstream of Vienna
(Tockner et al. 1998). Recognition of SGDE diversity, at least
on the basis of aquifer type, is essential for the recognition of
subterranean wetland types, and can aid identification of con-
servation priorities by locating probable biodiversity hotspots
(Dole-Olivier et al. 2009). In combination with distributional
data, a classification can guide the design of groundwater reserves
(Michel et al. 2009). Basing it on the ecohydrogeological
944 Marine and Freshwater Research
characteristics of connectivity to other ecosystems and aquifer
permeability explicitly recognises the features that deserve pro-
tection, both in ‘open’ systems when connectivity is high and the
integrity of adjacent surface ecosystems is also worthy of con-
servation, and in discrete habitats with low connectivity, such as
calcretes, where endemism is potentially high.
Informing environmental impact and other ecological
assessments
The consideration of subterranean fauna in the environmental
impact assessment of development proposals is formalised
only in Western Australia where guidance documents provide
advice on assessment protocols, sampling design and methods
(Environmental Protection Authority 2003, 2007). Discriminat-
ing patchiness among habitats is crucial for efficient sampling
design because it facilitates appropriate stratification of sampling
to capture the range of potential habitats and within-habitat
variation.
Habitat patchiness can indicate the likely presence of high
biodiversity assemblages or short-range endemics. Differences
in connectivity and permeability can indicate vulnerability to
anthropogenic contaminants and hydrological disturbance. These
characteristics may contribute to a typology of groundwater
‘landscapes’ for which indicator criteria may be developed
for monitoring ecological ‘health’ or the condition of SGDEs
(Steube et al. 2009). By using the tiered ecohydrogeological
approach suggested earlier, environmental impact and other
assessments could go beyond simply listing fauna and habitats
because associations with broad-scale and fine-scale attributes
could be sought. From these associations, the potential for
disruption of the groundwater regime or mechanisms that could
affect the fauna and/or ecological processes occurring in SGDEs
could be identified, helping to address a major research gap and
aiding in the effective management of groundwater resources.
Informing water planning
The Australian national water reforms require an environmental
allocation or provision in water resource plans. For ground-
water, this involves provision for the water needs of GDEs.
However, attention to determining the water needs of GDEs
has focussed on terrestrial systems (Land and Water Australia
2009). An ecohydrogeological approach to SGDEs would better
foster an understanding of groundwater habitats by informing
conceptual models of the connectivity between SGDEs and
other ecosystems, and of subsurface ecosystem function. It
would also guide efficient sampling and modelling designs for
estimating water requirements according to habitats present in
the water planning area. Where connectivity among habitats
is high, water requirements of different habitats are inevitably
linked. An ecohydrogeological approach would aid prediction
and understanding of the ecological effects of management
decisions and actions in ecosystems adjacent to SGDEs.
Conclusions and research needs
This review of Australian SGDEs reveals their substantial
ecological values, but also the extensive knowledge gaps and the
rudimentary level of our understanding of the drivers of sub-
surface ecological processes in Australia and overseas. Many
M. Tomlinson and A. J. Boulton
SGDEs deliver a range of goods and services, and through their
connections with other systems, impact on and are impacted by
them. Surface and groundwater systems are interconnected,
although this interconnection may be intermittent or pulsed,
depending on the groundwater regime and the volume and
degree of connection to recharge. Disturbances such as pollution
or management interventions either in SGDEs or connected
systems have flow-on effects, often with time lags that mask the
initial severity of the impacts.
Our proposed ecohydrogeological approach to understand-
ing SGDE diversity aims to assist in the effective management
of SGDEs and their ecosystem goods and services by acknow-
ledging the continua among habitats and focusing on the
mechanisms by which hydrology, hydrogeology and ecology
interact. Decision tools and standard methods and protocols
are urgently needed for monitoring and assessing indicators
of SGDE health and identifying high conservation value eco-
systems, and guiding SGDE-specific management actions to
maintain biodiversity, ecosystem function and water quality.
Research and surveys of SGDEs must be better coordinated with
standard national requirements for depositing voucher speci-
mens in museums and a central database comprising: (i) an atlas
of stygofaunal distribution across habitat types with collated
data on ranges of environmental parameters including depth
records; and (ii) records of stygofaunal taxa conforming to a
standard, nationally agreed terminology and including metadata
such as sampling methods, aquifer and habitat type and asso-
ciated details of water quality (e.g. conductivity, dissolved
oxygen). The value of an integrative spatial database in char-
acterising and evaluating patterns of biodiversity is illustrated
by the success of the PASCALIS project in western Europe
(Gibert et al. 2005) where, based on distributional data for
stygobitic taxa across six European countries, it has proved a
powerful tool for ranking and prioritising hotspots and evaluat-
ing knowledge gaps (Deharveng et al. 2009).
Much of the basic taxonomy and biology of Australian
stygobites remains to be elucidated. Little is known about basic
life-history characteristics such as longevity, number of eggs,
length of egg development and the ability to diapause. We must
learn more about the effects on biogeochemical processes and
stygofaunal communities of anthropogenic changes to ground-
water environments such as dewatering, contamination, extrac-
tion or artificial recharge, and other perturbations of the
groundwater regime. Without an ecohydrogeological frame-
work for setting the context for research or management plans
for SGDEs, synthesis of the current state of knowledge and
its applicability to assessing likely groundwater requirements
of different subterranean habitats is severely hampered. Any
framework must be continually reassessed for its validity and
usefulness and, where possible, the framework should be cap-
able of generating testable hypotheses about driving variables
and mechanisms that can be explored at the aquifer and
landscape scale during management interventions.
Acknowledgements
This paper is based on a review commissioned by the National Water
Commission in 2008. For valuable discussion and helpful comments on an
earlier document, we thank Andy Austin, Steve Cooper, Russell Crosbie,
Stefan Eberhard, Graham Fenwick, Hans Jürgen Hahn, Peter Hancock,
Subsurface groundwater dependent ecosystems
Stuart Halse, Bill Humphreys, David Le Maitre, Sarah Mika, Dean Olsen
and Ian Smith. Support is gratefully acknowledged from the Australian
Research Council and the ARC-funded Environmental Futures Network,
and from the Wentworth Group of Concerned Scientists (to M.T.).
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