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Marine and Freshwater Research, 2010, 61, 936–949

Ecology and management of subsurface groundwater

dependent ecosystems in Australia ] a review

Moya TomlinsonA,B and Andrew J. BoultonA

Ecosystem Management, University of New England, Armidale, NSW 2351, Australia.
Corresponding author. Email:

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 Australia 2009), but subsurface GDEs are routinely ignored in
for better groundwater management (Danielopol et al. 2003; ecological assessments for management, particularly in water
Humphreys 2006). Growing awareness that aquifers are dynamic planning, but also in conservation planning and environmental
ecosystems rather than simply underground water storages has impact assessment. This risks inadequate protection of environ-
prompted questions from resource managers on how to identify mental goods and services, which underpin the health and
and provide for the environmental values of groundwater. productivity of SGDEs and connected ecosystems.
Aquatic ecologists have focussed on surface water ecosystems, Here, we review the scattered literature on biodiversity and
largely leaving groundwater research and management to ecological processes in Australian SGDEs and list their ecosys-
hydrogeologists, although the tide is turning (e.g. a 2009 special tem services. To facilitate research and management of SGDEs,
issue of the Hydrogeological Journal focussed on integrating we propose an ecohydrological approach to understanding
ecology and hydrogeology). A review is timely because the lit- anthropogenic disturbance based on the connectivity of SGDEs
erature on the ecology of subsurface groundwater dependent to other ecosystems and aquifer permeability. We conclude with
ecosystems (SGDEs) is broad, poorly integrated and seldom research gaps evident from our review, emphasising those that
readily available to hydrogeologists or managers. We define an must be filled urgently to support wise management of this finite
SGDE as ‘an aquatic ecosystem occurring below the surface of resource in Australia. Many of these research gaps also exist
the ground that would be significantly altered by a change in the overseas and our review has relevance for SGDEs worldwide.
chemistry, volume and/or temporal distribution of its ground-
water supply’ (adapted from Parsons and Wentzel 2007).
Groundwater biodiversity in Australia
Australia’s national water reforms require an environmental
provision in water plans (Commonwealth of Australia 2004). Australian SGDEs harbour surprising biodiversity (Humphreys
However, environmental ‘flow’ setting for groundwater has 2008) of specialised groundwater fauna (stygobites sensu Gibert
received scant attention, although it is understood to involve et al. 1994) (Table 1). The groundwater environments are listed
identifying groundwater dependent ecosystems (GDEs) and in Table 1 as reported in the literature, but are not mutually
assessing the nature of their groundwater dependency (SKM exclusive; for example, calcrete aquifers may or may not be
2001). Some progress has been made with identification and karstified, and calcrete deposits are often interdigitated with
assessment of surface GDEs (e.g. groundwater dependent 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
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 and caves. In Europe, the number of endemic stygofauna
aquifers (Table 1), but this may be partly a result of uneven (groundwater invertebrates) is greater in karstic systems than in
sampling intensity across the different aquifer types. alluvial aquifers, perhaps because the greater isolation of karstic
Survey effort in Australia is patchy and incomplete, but habitats facilitates speciation (Danielopol et al. 2000). As eastern
rapidly improving with many exploratory baseline surveys Australian karst has only been sparsely surveyed (Thurgate et al.
being conducted, particularly in Western Australia as part of 2001), it is likely that much stygobitic diversity remains un-
the environmental impact assessment for mining developments documented. Furthermore, a great deal of information is not
(Humphreys 2008; Eberhard et al. 2009; Hancock and Boulton readily accessible because it is in unpublished consultancy or
2009). Existing survey work covers some coastal and inland government reports or in individual researcher’s records. Apparent
alluvial, fractured rock and arid-zone karstic and calcrete patterns of biodiversity reflect sampling effort and available
938 Marine and Freshwater Research M. Tomlinson and A. J. Boulton

taxonomic interest and expertise (Eberhard et al. 2009); un- conditions (e.g. aridity); and truncated food webs with no
explored groups may be equally diverse. primary producers. Characteristic of the Australian stygofauna
As in Europe (Deharveng et al. 2009), crustaceans including are taxa that are relicts of ancient lineages and have very limited
isopods, copepods, ostracods and amphipods dominate the distributions. The anchialine fauna of Cape Range (Fig. 1) is an
Australian stygofauna. For example, surveys to date have example of the persistence of phyletic relictual fauna hypothe-
revealed a new genus of isopod (Wilson 2003), over 110 species sised to derive from populations already inhabiting subterranean
of ostracod (Reeves et al. 2007) in the Pilbara region alone habitats before the break-up of Gondwana (Humphreys 2000).
(Fig. 1), and 31 species of copepod from the Murchison region, This distinctive fauna includes the only southern hemisphere
part of the Yilgarn Craton (Karanovic 2004). Amphipods are representatives of the copepod order Misophrioida (Jaume et al.
widespread and exhibit cryptic diversity and a high degree of 2001), another crustacean order Thermosbaenacea (Poore and
endemism (Cooper et al. 2007; Finston et al. 2007; Bradford Humphreys 1992) and the class Remipedia (Lasionectes exleyi
et al. 2010). Of the crustacean superorder Syncarida, anaspids (Yager and Humphreys 1996), known from a single water-filled
are restricted to southern Australia (Hobbs 2000). The bath- cave at Cape Range). The only Australian records of the
ynellids are well represented and largely undescribed, although peracarid crustacean order Spelaeogriphacea are two species
the Western Australian fauna has received some attention (e.g. (of four globally) from the Fortescue valley in the Pilbara
Cho et al. 2005, 2006; Guzik et al. 2008). A wide range of other (Fig. 1; Poore and Humphreys 1998, 2003).
taxa is represented in Australia, including over 90 new species of Harvey (2002) defined short-range endemic species as those
stygobitic dytiscid diving beetles (Watts and Humphreys 2006; with a range of less than 10 000 km2, and noted that most short-
Watts et al. 2007) and two species of fish (Humphreys 1999). range endemic species possess characteristics such as limited
The diversity of subsurface microbial, fungal and protozoan dispersal ability and confinement to discontinuous habitats.
communities is virtually unexplored in Australia. However, Eberhard et al. (2009) suggest that 1000 km2 may be a more
some biochemically novel, chemoautotrophic communities satisfactory threshold for short-range endemism of stygobites.
consisting of mucoid sheets and dependent on nitrite oxidation The high diversity of short-range endemic dytiscid diving
have been described from karst of the Nullarbor Plain (Fig. 1; beetles in calcrete aquifers in the Pilbara (Watts and Humphreys
Holmes et al. 2001). 2006) has been attributed to multiple independent colonisations
Patterns of subterranean faunal biodiversity are the product of aquifers that subsequently became subterranean ‘islands’
of four characteristics (Gibert and Deharveng 2002): low isolated by the onset of aridity (Cooper et al. 2002; Leys et al.
number of lineages owing to the ecological filter of the transition 2003). Studies of the mitochondrial DNA of amphipods (Cooper
to lightless environments; high endemism owing to habitat et al. 2007; Bradford et al. 2010), oniscidean isopods (Cooper
fragmentation; high level of relict taxa owing to persistence of et al. 2008) and parabathynellids (Guzik et al. 2008) from these
subsurface refugia over long periods of unfavourable surface calcretes support this interpretation.

valley Kimberley

Great Artesian Basin

Swan Nullarbor Plain

Yilgarn Tamworth

1000 km

Fig. 1. Outline map of Australia showing the locations mentioned in the text.
Subsurface groundwater dependent ecosystems 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
Terrestrial Riparian multiple spatial scales and habitat types grade into each other.
vegetation vegetation Furthermore, each aquifer type is unlikely to be a discrete
Freshwater habitat harbouring a distinctive fauna. In some environments,
psammo- such as calcretes and mound springs, short-range endemism is
littoral high, yet where connections between habitats exist there may be a
SGDEs broad overlap of taxa, although richness and abundances differ.
Except for large-bodied taxa such as fish that require large
Marine voids, stygofauna from the Pilbara and adjacent areas are found
zone wherever groundwater environments provide suitable habitat
Marine (Eberhard et al. 2005), including in porous, karstic and frac-
Marine and upwelling Surface tured-rock aquifers as well as in the hyporheic zone and springs.
estuarine and intrusion waters The tendency to habitat generality by many taxa indicates that
(Springs, rivers,
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
Fig. 2. Subsurface groundwater dependent ecosystems (centre) are linked
through ecotones (speckled area) to other ecosystems (outer circle).
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
Life-history adaptations by stygofauna to the relatively more other likely habitats is crucial because it affects recolonisation
stable aquifer environment include fewer but larger eggs, sources and pathways, the potential for endemism, and the
prolonged egg development (Rouch and Danielopol 1999) and magnitude and type of repercussions for other ecosystems.
greater longevity compared with phyletically related surface- Subsurface groundwater dependent ecosystems are often
dwelling taxa (Dole-Olivier et al. 2000). These data are all from hydrologically and ecologically connected to terrestrial and
studies of European fauna. Although equivalent physiological aquatic surface ecosystems through transition zones including
adaptations and life histories may be assumed for Australian the hyporheic zone, the vadose zone, marine upwelling and
stygofauna, research is needed to confirm this assumption. intrusion zones, and the psammolittoral zone (Fig. 2). There may
These life-history adaptations to the relatively stable aquifer also be direct connections between SGDEs, for example, where
environment would not be advantageous in a situation of rapid an alluvial aquifer overlies or interdigitates with another aquifer
environmental change such as anthropogenic water level fluc- type such as calcrete or fractured rock (Eberhard et al. 2009).
tuations. Diapause in unfavourable environmental conditions The interfaces between habitats are usually characterised by
is known for surface-water species of taxa with groundwater spatially and temporally dynamic gradients in environmental
representatives (e.g. copepods; Hairston and Caceres 1996), conditions that defy precise delineation of ecosystem bound-
but has not yet been recorded in groundwater forms. Fauna in aries. These ‘dynamic ecotones’ (Vervier et al. 1992) are zones
unconfined aquifers are potentially vulnerable to stranding if of exchange of materials and energy and potential pathways for
the amplitude and frequency of watertable fluctuations are faunal dispersal and transmission of contaminants.
increased by groundwater extraction. Microcosm experiments The hyporheic zone is the saturated sediments below and
on stygofauna from bores near Tamworth, NSW (Fig. 1), alongside stream beds where surface water and groundwater
indicate that small-bodied fauna such as copepods are able mix (White 1993). In the arid zone, the hyporheic fauna of
to follow declining water levels, but larger animals such as ephemeral streams is groundwater dependent most of the time,
amphipods become stranded (Tomlinson 2009). 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
Habitat diversity in the subsurface support terrestrial vegetation (O’Grady et al. 2009), fauna in the
Widespread perceptions of reduced habitat heterogeneity, vadose zone can be considered groundwater dependent because
low productivity and unfavourable environmental conditions vadose zone moisture is discharging groundwater. In karstic
(e.g. low dissolved oxygen, high sulfur) belie the true diversity aquifers, the vadose zone is a complex rock–soil interface
of aquifer habitats and the habitat differences that are key to termed epikarst (i.e. ‘skin of karst’; Bakalowicz 2004). The
appreciating the subtle complexities of subterranean ecology. epikarst in Europe (Pipan and Culver 2007) and North America
Despite the shared characteristics of being subterranean and (Pipan et al. 2006) harbours a diverse stygofauna distinct
lightless, karstic, calcrete, alluvial, fractured rock and other from the fauna found in the saturated zone. This habitat has
groundwater environments differ in many ecologically relevant been sparsely sampled in Australia, but stygofauna have been
features. For example, subsurface environmental conditions recorded in the vadose infiltration waters of karstic caves in
may exhibit steep gradients in physico-chemical conditions, and 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


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

Groundwater discharge contributes to river flow (Wood related to the flow patterns of pollutants (Malard et al. 1994,
et al. 2005; Cook et al. 2006), supports instream and riparian 1996) and to aquifer hydrodynamics (Dumas et al. 2001).
communities (Boulton and Hancock 2006), wetlands (McCarthy A dominance of stygobites indicates low surface water inputs,
2006), and aquatic communities in caves (Eberhard 2004), and may indicate the absence of nitrate-enriched surface water
springs and springbrooks (Meyer et al. 2003), sustains terrestrial in aquifers (Claret et al. 1999).
vegetation (Lamontagne et al. 2005a; O’Grady et al. 2009) If stygofauna are more sensitive than surface water fauna to
and supports some estuarine and marine ecosystems (Linderfelt chemical pollutants (Plénet 1999; Mosslacher 2000), ground-
and Turner 2001; Dale and Miller 2007). Grazing of biofilms water quality criteria based on the responses of surface water
by stygofauna is postulated to prevent overgrowth of biofilm organisms may be insufficient to protect groundwater systems
and consequent sediment clogging, as demonstrated for a soil (Hose 2005). The use of stygofauna as biomonitors of heavy
flagellate by Mattison et al. (2002). Benthic and hyporheic fauna metal contamination has been explored in Europe (e.g. Plénet
achieve similar outcomes through mechanical bioturbation and et al. 1996; Canivet and Gibert 2002), but there is no equivalent
pelletisation (e.g. Mermillod-Blondin et al. 2003; Nogaro et al. work in Australia.
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 Consideration of scale in SGDE management
by migration into moist or saturated refugia including SGDEs Only in the past decade have Australian groundwater managers
(Boulton et al. 1992; Harris et al. 2002). Fish in floodplains become aware of ecological considerations such as the water
of the east Kimberley retreat to karst sinkholes during the dry needs of GDEs and the maintenance of groundwater ecosystem
season (Humphreys 1995). Groundwater discharge into estu- function (Tomlinson and Boulton 2008). Groundwater man-
aries may provide refuge zones for salt-sensitive species during agement must be across ecologically relevant scales because
periods of hypersaline conditions associated with reduced river these environments are dynamic ‘open’ systems where biolo-
discharge during droughts (Taylor et al. 2006). On an evolu- gical and geochemical interactions and transformations occur
tionary scale, aquifers have provided refugia from changing at a range of scales. At a broad scale (103 m), resource avail-
environmental conditions on the surface, including the onset of ability in the subsurface is determined by aquifer type; geology
aridity in Australia (Cooper et al. 2002; Finston et al. 2007). largely determines the porosity and contributes to the hydraulic
Subsurface groundwater dependent ecosystems provide conductivity of the aquifer matrix. This affects the rate of
crucial regulating services such as flood control and erosion groundwater recharge as well as ecological aspects such as the
prevention. Aquifer storage of run-off and stream flow is available physical living space for fauna, the entrainment of
particularly significant in zones of strong groundwater–surface organic matter and the supply of nutrients and dissolved oxygen
water connections such as river banks and floodplains (Brunke (e.g. Ward et al. 1994; Rouch and Danielopol 1999).
and Gonser 1997; Sophocleous 2002). This ‘buffering effect’ On finer scales (10 3 m), exchange processes between
reduces the flashiness of stream discharge, with important surface and groundwater are ecologically relevant (Sophocleous
hydrological repercussions for surface fauna and processes 2002). These are often patchy, where zones of higher trans-
(Bunn and Arthington 2002). missivity (e.g. downwelling zones in stream channels) can
Groundwater has strong cultural values in Indigenous Aus- promote the supply of organic material that is the basis of
tralia. Stories associated with groundwater-related sites such as many subsurface food webs (Datry et al. 2005; Hancock et al.
springs, mound springs, caves and native wells played a role 2005) to create ‘hot spots’ of biodiversity and/or activity.
in traditional law and protocols (Moggridge 2007). In the arid Fine-scale spatial variability in biogeochemical processes
zone, groundwater in streambeds supplies drinking water and and faunal distribution, abundance and richness coupled with
supports important ‘bush tucker’ such as the plant Ipomoea sp. shifting physico-chemical gradients create a rich mosaic of
listed under the Commonwealth Environment Protection and microenvironments (Pospisil 1994; Coineau 2000), constitut-
Biodiversity Conservation Act (Department of the Environment ing a set of functional mesohabitats that may be distinguished
Water Heritage and the Arts 2008). The Indigenous relationship by hydraulic and physical characteristics (Brunke et al. 2001;
with aquatic systems may be understood as a socio-ecological Kasahara et al. 2009). These characteristics are likely to be
relationship equivalent to kinship relations of obligation and hierarchically scaled, rather like a series of filters controlling
care (Jackson 2006), suggesting that contemporary Aboriginal faunal distribution (Poff 1997). For example, Reeves et al.
communities have cultural reasons for involvement in ground- (2007) found that subregional differentiation in ostracod
water management. genera in the Pilbara, Western Australia, was determined
Stygofauna are potential indicators of ecosystem condition primarily by altitude, then surface drainage basin, and finally
and the integrity of fundamental ecological processes in ground- aquifer. Conversely, stygofaunal composition within an allu-
waters. Despite pleas for ecosystem-level management (e.g. vial aquifer near Perth, Western Australia (Fig. 1), did not
Likens et al. 2009), current river health assessment in Australia match geological, chemical or topographical features, but was
does not consider the condition of hyporheic zones (Boulton better characterised by finer-scale abiotic conditions, includ-
2000; Hancock 2002) or connected alluvial aquifers. Inclusion ing dissolved oxygen and temperature (Schmidt et al. 2007).
of these components would enhance the robustness of river Danielopol et al. (2004) urged the European Union Ground-
health assessment (Reid and Brooks 2000), especially in ephe- water Directive to account for the different vulnerabilities of
meral arid zone rivers with subsurface flow. In aquifers, the alluvial sediments and karstic systems, and this broad division
relative abundance of surface water and groundwater taxa can be of aquifer types was the basis for an assessment of groundwater
Subsurface groundwater dependent ecosystems Marine and Freshwater Research 943

biodiversity across six European regions (Dole-Olivier et al. heterogeneity in substrate characteristics produces gradients or
2009). Meanwhile, in response to the management requirements patchiness in the availability of habitat and food.
of the EU Water Framework Directive, Dahl et al. (2007) Thus, we argue that the most effective typology of SGDEs
proposed a multi-scale typology of groundwater–surface water will be based on ecohydrogeological principles relating aquifer
interactions based on geomorphic, geological and hydrological characteristics (e.g. porosity and permeability), groundwater
concepts reflecting functional linkages and controlling flow regime and connectivity across aquifers and to adjacent ecosys-
processes at reducing scales. On a catchment scale (flow paths tems, and will be arranged in a tiered hierarchy that acknow-
45 km) groundwater flow was classified by regional geomor- ledges how the broad-scale ‘filters’ (sensu Poff 1997) of climate,
phology; on an intermediate or reach scale (1–5 km) ground- surface drainage and recharge, geology and topography will
water–riparian interactions were classified by hydrogeology; and govern finer-scale aspects such as porosity and groundwater
at a local scale of 10–1000 m classification was based on flow flow. In turn, these broad-scale and fine-scale aspects determine
path distribution. Flow regime delineates groundwater bodies and ecological processes and habitat availability, influence produc-
illustrates their vulnerability to pollution. Vulnerability assess- tivity and stygobite diversity, and control the provision of
ment involves considering the travel time of infiltrating water, the groundwater ecosystem goods and services, as reviewed above.
effectiveness of the hydrological connection between surface and Research is now needed on how these aspects and filters interact
groundwater, and the hydrogeological attributes of the aquifer in different SGDEs worldwide, and how aquifer characteristics,
materials (Quevauviller 2008). groundwater regime and hydrological connectivity affect eco-
Hahn and Fuchs (2009) applied a scale-based, ecologically logical features and water quality in SGDEs.
focussed hierarchical typology approach to the identification
of groundwater habitats in the south-western German state of
Using an ecohydrogeological approach in management
Baden-Württemberg (37 750 km2). The state was separated into
regional geological units that were subdivided into geohydro- Guiding conservation planning
logical groups (aquifer types). The stygofaunal community Some Australian subterranean species and several groundwater
structure broadly matched the geohydrological groups, and dependent communities are listed under biodiversity protection
was more finely associated with subtypes characterised by legislation, but this mechanism is necessarily only applicable to
differences in porosity and hydraulic conductivity, which influ- species and communities under a demonstrable and significant
enced the hydrological exchange and amount of living space. 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
Is a typology of SGDEs needed? biodiversity protection is potentially afforded through pro-
Classification of potential habitats in SGDEs may help predict tected area systems. Planning for reserve networks relies on
stygofaunal biodiversity, abundance, distributions and com- habitat classification schemes such as those developed to
munity structure and would therefore be useful in determining implement the Ramsar Convention (Ramsar Convention on
priorities for surveys and management applications, such as Wetlands 1971), but this wetland classification subsumes all
assessing vulnerability to risks and identifying conservation subterranean wetlands under the category ‘Karst and other
priorities (Castellarini et al. 2007a, 2007b). However, few subterranean hydrological systems, inland’, effectively blur-
habitats are delineated by discrete boundaries, and the cate- ring the distinctions between habitat types. The classification
gories in any typology are defined for a particular purpose and used by the Directory of Important Wetlands in Australia nar-
reflect hypotheses about relevant organising principles. The rows this category to ‘Inland, subterranean karst wetlands’
dividing lines therefore differ according to the intended appli- (Environment Australia 2001). Work is underway to develop
cation, and in every case are fuzzy in space and time. A typology an Australian National Aquatic Ecosystem classification which
used as a fixed classification for all applications will be mis- will include a broader range of attributes and allow recognition
leading, but when applied as a heuristic tool (e.g. Hahn 2009) of the diversity of SGDEs.
may offer insights and guidance to management decisions. This Although some subterranean wetlands are serendipitously
cautionary note is particularly pertinent for the management of included in the existing protected areas systems, most occur in
aquatic ecosystems owing to their inherently high connectivity areas of high and competing demands for water and mineral
(Nel et al. 2009). Any categorisation of SGDEs in Australia, resources. The creation of a national park based on subterranean
although based on an initial identification of broad aquifer types ecological values seems unlikely in Australia for any but
(e.g. karstic, fractured rock, alluvial), must then consider the spectacular cave ecosystems. However, a precedent exists
range and variability in climatic conditions across the continent in Europe with the designation in 1996 of the Alluvial
(Stern et al. 2000) because these will determine patterns of Zone National Park, protecting the alluvial landscape in a free-
recharge and discharge, strong drivers of spatial and temporal flowing section of the Danube River downstream of Vienna
differences in groundwater regime and subsurface resource (Tockner et al. 1998). Recognition of SGDE diversity, at least
supply, particularly where connectivity to the surface is high. on the basis of aquifer type, is essential for the recognition of
Degrees of porosity determine available living space for fauna subterranean wetland types, and can aid identification of con-
and biofilms, place physical constraints on faunal size and servation priorities by locating probable biodiversity hotspots
food particles (e.g. particulate organic matter) and affect (Dole-Olivier et al. 2009). In combination with distributional
hydraulic conductivity and therefore the delivery rate of oxygen, data, a classification can guide the design of groundwater reserves
particulate organic matter and solutes. On a finer scale, localised (Michel et al. 2009). Basing it on the ecohydrogeological
944 Marine and Freshwater Research M. Tomlinson and A. J. Boulton

characteristics of connectivity to other ecosystems and aquifer SGDEs deliver a range of goods and services, and through their
permeability explicitly recognises the features that deserve pro- connections with other systems, impact on and are impacted by
tection, both in ‘open’ systems when connectivity is high and the them. Surface and groundwater systems are interconnected,
integrity of adjacent surface ecosystems is also worthy of con- although this interconnection may be intermittent or pulsed,
servation, and in discrete habitats with low connectivity, such as depending on the groundwater regime and the volume and
calcretes, where endemism is potentially high. degree of connection to recharge. Disturbances such as pollution
or management interventions either in SGDEs or connected
Informing environmental impact and other ecological systems have flow-on effects, often with time lags that mask the
assessments initial severity of the impacts.
The consideration of subterranean fauna in the environmental Our proposed ecohydrogeological approach to understand-
impact assessment of development proposals is formalised ing SGDE diversity aims to assist in the effective management
only in Western Australia where guidance documents provide of SGDEs and their ecosystem goods and services by acknow-
advice on assessment protocols, sampling design and methods ledging the continua among habitats and focusing on the
(Environmental Protection Authority 2003, 2007). Discriminat- mechanisms by which hydrology, hydrogeology and ecology
ing patchiness among habitats is crucial for efficient sampling interact. Decision tools and standard methods and protocols
design because it facilitates appropriate stratification of sampling are urgently needed for monitoring and assessing indicators
to capture the range of potential habitats and within-habitat of SGDE health and identifying high conservation value eco-
variation. systems, and guiding SGDE-specific management actions to
Habitat patchiness can indicate the likely presence of high maintain biodiversity, ecosystem function and water quality.
biodiversity assemblages or short-range endemics. Differences Research and surveys of SGDEs must be better coordinated with
in connectivity and permeability can indicate vulnerability to standard national requirements for depositing voucher speci-
anthropogenic contaminants and hydrological disturbance. These mens in museums and a central database comprising: (i) an atlas
characteristics may contribute to a typology of groundwater of stygofaunal distribution across habitat types with collated
‘landscapes’ for which indicator criteria may be developed data on ranges of environmental parameters including depth
for monitoring ecological ‘health’ or the condition of SGDEs records; and (ii) records of stygofaunal taxa conforming to a
(Steube et al. 2009). By using the tiered ecohydrogeological standard, nationally agreed terminology and including metadata
approach suggested earlier, environmental impact and other such as sampling methods, aquifer and habitat type and asso-
assessments could go beyond simply listing fauna and habitats ciated details of water quality (e.g. conductivity, dissolved
because associations with broad-scale and fine-scale attributes oxygen). The value of an integrative spatial database in char-
could be sought. From these associations, the potential for acterising and evaluating patterns of biodiversity is illustrated
disruption of the groundwater regime or mechanisms that could by the success of the PASCALIS project in western Europe
affect the fauna and/or ecological processes occurring in SGDEs (Gibert et al. 2005) where, based on distributional data for
could be identified, helping to address a major research gap and stygobitic taxa across six European countries, it has proved a
aiding in the effective management of groundwater resources. powerful tool for ranking and prioritising hotspots and evaluat-
ing knowledge gaps (Deharveng et al. 2009).
Informing water planning Much of the basic taxonomy and biology of Australian
stygobites remains to be elucidated. Little is known about basic
The Australian national water reforms require an environmental
life-history characteristics such as longevity, number of eggs,
allocation or provision in water resource plans. For ground-
length of egg development and the ability to diapause. We must
water, this involves provision for the water needs of GDEs.
learn more about the effects on biogeochemical processes and
However, attention to determining the water needs of GDEs
stygofaunal communities of anthropogenic changes to ground-
has focussed on terrestrial systems (Land and Water Australia
water environments such as dewatering, contamination, extrac-
2009). An ecohydrogeological approach to SGDEs would better
tion or artificial recharge, and other perturbations of the
foster an understanding of groundwater habitats by informing
groundwater regime. Without an ecohydrogeological frame-
conceptual models of the connectivity between SGDEs and
work for setting the context for research or management plans
other ecosystems, and of subsurface ecosystem function. It
for SGDEs, synthesis of the current state of knowledge and
would also guide efficient sampling and modelling designs for
its applicability to assessing likely groundwater requirements
estimating water requirements according to habitats present in
of different subterranean habitats is severely hampered. Any
the water planning area. Where connectivity among habitats
framework must be continually reassessed for its validity and
is high, water requirements of different habitats are inevitably
usefulness and, where possible, the framework should be cap-
linked. An ecohydrogeological approach would aid prediction
able of generating testable hypotheses about driving variables
and understanding of the ecological effects of management
and mechanisms that can be explored at the aquifer and
decisions and actions in ecosystems adjacent to SGDEs.
landscape scale during management interventions.
Conclusions and research needs Acknowledgements
This review of Australian SGDEs reveals their substantial This paper is based on a review commissioned by the National Water
ecological values, but also the extensive knowledge gaps and the Commission in 2008. For valuable discussion and helpful comments on an
rudimentary level of our understanding of the drivers of sub- earlier document, we thank Andy Austin, Steve Cooper, Russell Crosbie,
surface ecological processes in Australia and overseas. Many Stefan Eberhard, Graham Fenwick, Hans Jürgen Hahn, Peter Hancock,
Subsurface groundwater dependent ecosystems Marine and Freshwater Research 945

Stuart Halse, Bill Humphreys, David Le Maitre, Sarah Mika, Dean Olsen diversity in a calcrete aquifer in Western Australia’s arid zone.
and Ian Smith. Support is gratefully acknowledged from the Australian Molecular Ecology Resources 10, 41–50. doi:10.1111/J.1755-0998.
Research Council and the ARC-funded Environmental Futures Network, 2009.02706.X
and from the Wentworth Group of Concerned Scientists (to M.T.). Brunke, M., and Gonser, T. (1997). The ecological significance of exchange
processes between rivers and groundwater. Freshwater Biology 37,
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