Subsurface Groundwater Dependent Ecosystems: a review of their biodiversity, ecological processes and ecosystem services

Moya Tomlinson and Andrew Boulton University of New England
Waterlines Occasional Paper No 8, October 2008


This paper is part of a series of works commissioned by the National Water Commission on key water issues. This work has been undertaken by the University of New England on behalf of the National Water Commission.

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Online: ISBN 978-1-921107-67-2 Subsurface groundwater dependent ecosystems: a review of their biodiversity, ecological processes and ecosystem services, October 2008 Authors: Moya Tomlinson and Andrew Boulton

Published by the National Water Commission 95 Northbourne Avenue Canberra ACT 2600 Tel: 02 6102 6088 Email:

Date of publication: October 2008

Cover design by: AngelInk Cover photo courtesy of Moya Tomlinson

This paper is presented by the National Water Commission for the purpose of informing discussion and does not necessarily reflect the views or opinions of the Commission.


National Water Commission position statement........................................................................ iii
Acknowledgements ....................................................................................................................v
Executive summary
1 Introduction ............................................................................................................................ 1
1.1 Aims and scope of this review........................................................................................ 1
1.2 What are SGDEs?.......................................................................................................... 2
1.3 Brief description of the main occurrences of SGDEs..................................................... 5
1.4 A fundamental property of SGDEs: connection to other ecosystems............................ 8
1.5 Characteristics of SGDEs and their fauna ..................................................................... 9
1.6 Drivers of groundwater ecology ................................................................................... 10
2 Biodiversity values of SGDEs.............................................................................................. 12
2.1 Defining biodiversity ..................................................................................................... 12
2.2 The value of biodiversity .............................................................................................. 12
2.3 Subterranean biodiversity ............................................................................................ 13
2.4 Characteristics of stygobitic fauna ............................................................................... 14
2.5 Australian stygobitic biodiversity .................................................................................. 15
3 Subsurface ecological processes ........................................................................................ 19
4 Provision of goods and services.......................................................................................... 21
4.1 Provisioning services ................................................................................................... 21
4.2 Supporting services...................................................................................................... 21
4.3 Regulating services...................................................................................................... 23
4.4 Cultural services........................................................................................................... 24
5 Management of SGDEs....................................................................................................... 26
5.1 Conservation ................................................................................................................ 26
5.2 Threatening processes and SGDEs............................................................................. 27
5.3 The potential impact of climate change ....................................................................... 28
5.4 Current policy setting in Australia................................................................................. 30
5.5 International groundwater policy: Europe .................................................................... 38
5.6 International groundwater policy: South Africa ............................................................ 39
6 Knowledge needs and research directions ......................................................................... 40
6.1 What is the appropriate management scale for SGDEs? ............................................ 43
6.2 A proposed typology of SGDEs ................................................................................... 44
6.3 Investigations of functional groups............................................................................... 49
6.4 What level of taxonomic identification is necessary?................................................... 51
6.5 Measuring biodiversity and monitoring management action........................................ 51
6.6 Priority research directions........................................................................................... 52
7 Conclusion ........................................................................................................................... 55
8 References .......................................................................................................................... 56
Glossary................................................................................................................................... 75



List of tables

Table 1: Characteristics of groundwater environments and implications for groundwater biodiversity and ecology.................................................................................................... 9
Table 2: Stygobitic biodiversity in Australia ............................................................................. 16
Table 3: Ecosystem services provided by groundwater .......................................................... 21
Table 4: Legislation and policy addressing NWI requirements regarding environmental water
........................................................................................................................................ 30
Table 5: NWI objectives and actions relevant to environmental management of groundwater,
and actions reported in jurisdictional NWI implementation plans ................................... 33
Table 6: Knowledge needed to address NWI objectives, and suggested research questions 41
Table 7: Suggested SGDE typology........................................................................................ 47

List of figures
Figure 1: Conceptual model of factors influencing the biotic composition of SGDEs ............... 1
Figure 2: Location of regions and places referred to in the text ................................................ 5
Figure 3: SGDEs (centre) are linked through ecotones (speckled area) to other ecosystems
(outer circle) ...................................................................................................................... 8
Figure 4: A classification of groundwater species based on their affinity to groundwater
habitats............................................................................................................................ 13
Figure 5: A new genus of bathynellid syncarid........................................................................ 15
Figure 6: Conceptual model of anthropogenic impacts on groundwater bodies ..................... 39
Figure 7: The extremely coarse scale of identification of GDEs within groundwater
management units in the Australian Water Resources 2005 assessment ..................... 43
Figure 8: Classification of major climate types in Australia ..................................................... 48
Figure 9: Response curves...................................................................................................... 50

List of boxes
Box 1: A functional definition of groundwater ............................................................................ 3
Box 2: Attributes of the groundwater water regime (GWR) (SKM 2001)................................... 3
Box 3: Classes of GDE (Eamus et al. 2006) ............................................................................. 3
Box 4: Subsurface groundwater dependent ecosystem............................................................ 4
Box 5: Resistance and resilience .............................................................................................. 7
Box 6: Values served by biodiversity conservation ................................................................. 12
Box 8: Adaptations to subsurface groundwater habitats ......................................................... 14
Box 9: Nitrogen processes in groundwater ............................................................................. 19
Box 10: Case study 1 – Jewel Cave Western Australia .......................................................... 25
Box 11: EPBC Act listing of stygofaunal species and groundwater-dependent ecological
communities.................................................................................................................... 26
Box 12: Threatening processes in SGDEs.............................................................................. 27
Box 13: Symptoms of hydroschizophrenia .............................................................................. 31
Box 15: Necessary policy actions............................................................................................ 40
Box 16: Case study 2: An alluvial aquifer in temperate Australia – The Peel alluvium, NSW 45
Box 17: Case Study 2: An alluvial aquifer in arid Australia – Alice Springs Town Basin, NT . 46
Box 18: Understanding the groundwater resource.................................................................. 53



National Water Commission position Water-dependent ecosystems
Water-dependent ecosystems in Australia Water-dependent ecosystems include wetlands, floodplains, riparian areas, estuaries and springs. They provide many important services including provision of good quality water for irrigation and domestic use, habitat for fish and other aquatic fauna and flora, removal of wastes and contaminants, and aesthetic, cultural and recreational benefits. Without adequate and timely water these ecosystems lose their capacity to provide such services. In some cases, the losses may be irreversible; in others, they may be difficult and costly to reverse. Under current conditions, many significant water-dependent ecosystems are under threat. Commitments under the National Water Initiative to water-dependent ecosystems Striking a balance between water for consumptive uses and water for ecosystem health—so that environmental, social and economic outcomes are optimised—is integral to the National Water Initiative Agreement. Water planning is the fundamental means for achieving this balance. Overallocated water systems need to be restored to environmentally sustainable levels of extraction; in other systems, crucial environmental assets and ecosystem services need to be protected. The National Water Initiative calls for: • environmental water to enjoy the same security as water for consumptive uses • environmental water managers to be established and equipped with the necessary authority and resources • water market and trading arrangements to protect the needs of the environment • environmental water to be included in water accounts and audited • periodic assessments of river and wetland health to be conducted so that adaptive management can be undertaken on an evidence basis. Progress on water-dependent ecosystems The National Water Commission’s 2007 First Biennial Assessment of Progress in the Implementation of the National Water Initiative found that all states had made statutory provision for water to meet environmental and public benefit outcomes within water plans, however: • over-allocated systems were not always adequately identified • environmentally sustainable levels of extraction were poorly defined • there was considerable variability in the quality of the science underpinning water plans • in many cases the trade-offs between environmental and consumptive uses were not transparent • there was often a lack of specificity in the environmental outcomes. The Commission considers that the protection of threatened water-dependent ecosystems, including the recovery of overallocated systems, continues to be a major challenge in implementing the National Water Initiative Agreement. The Commission’s water-dependent ecosystems activities Over the past three years, the focus of Commission activities has been on filling knowledge gaps and promoting science to support good decisions about environmental water. These activities have included: • commissioning the synthesis of existing knowledge about specific aspects of waterdependent ecosystems and their management



• • • •

commissioning scoping studies to identify critical knowledge gaps and provide guidance on research priorities providing grants to research programs addressing issues such as the formation of acid sulfate sediments, water requirements for native fish populations and the use of aerial surveys of waterbirds as indications for wetland health supporting environmental water managers by establishing a ‘community of practice’ where they can share experiences undertaking trials of a national framework for assessing river and wetland health (FARWH), with the intention that an agreed framework will be delivered in 2011.

Future directions for water-dependent ecosystems The Commission will continue to build on these activities. However improved knowledge alone will not ensure that environmental outcomes are achieved. The Commission has therefore adopted the following six priorities to guide future work involving the management of water-dependent ecosystems: 1. Help develop and implement national guidelines and procedures for determining environmentally sustainable levels of extraction of water. A nationally agreed method will expedite the formulation of water plans that protect water-dependent ecosystems and include a pathway to recover overallocated systems. The methods will include guidelines for establishing clear environmental outcomes. 2. Pursue an agreed national inventory of over-allocated water systems together with commitments by governments to return them to sustainable levels of extraction. Identifying overallocated systems and recording agreed actions to recover the water needed to restore sustainability is central to achieving environmental outcomes contained in the NWI. 3. Improve the security of environmental water. In spite of the legislation now passed in all jurisdictions, environmental water allocations often lack specificity and there is uncertainty around the status and security of environmental water holdings. 4. Support more effective management of environmental water. There are many shortcomings in the governance and operations of environmental water managers. Statutory empowerment, funding, skills and access to science, data and best practice guidelines all require urgent attention. The development of a national community of practice in environmental water management is an important initiative that will support these water managers. 5. Strengthen the role of adaptive management of environmental water. Recent work commissioned by the Commission1 showed there is a deficiency in monitoring and reporting on plan implementation. This is a significant weakness when coupled with gaps in ecological knowledge and the occurrence of climatic conditions outside the planned-for circumstances. More systematic monitoring and reporting is essential to enable the water management regime to be adapted intelligently in the light of experience. 6. Implement the Framework for the Assessment of River and Wetland Health. While the Commission will continue to support the implementation of the Framework for the Assessment of River and Wetland Health, its successful adoption rests with the parties to the National Water Initiative Agreement. By pursuing these priorities, the Commission will play its part in promoting the enduring objective of the National Water Initiative to manage water–dependent ecosystems to best effect. We urge the parties to the National Water Initiative Agreement to do likewise. National Water Commission

1 September 2008


Hamstead M., Baldwin, C. and O’Keefe, V. (2008) Water allocation planning in Australia – current practices and lessons learned. Waterline Occassional Paper No. 6, April 2008. National Water Commission.




For valuable discussion, additional references and helpful comments on drafts we thank Andy Austin (University of Adelaide), Steve Cooper (South Australian Museum), Russell Crosbie (CSIRO), Stefan Eberhard (Subterranean Ecology), Graham Fenwick (National Institute of Water and Atmospheric Research, New Zealand), Hans Jürgen Hahn (University of Koblenz-Landau, Germany), Peter Hancock (University of New England), Stuart Halse (Bennelongia Pty. Ltd.), Bill Humphreys (Western Australian Museum), David Le Maitre (Council for Scientific and Industrial Research, South Africa), Sarah Mika (University of New England), Dean Olsen (Cawthron Institute, New Zealand) and Ian Smith (Department of Natural Resources, Environment and the Arts, Northern Territory Government). Support is gratefully acknowledged from the Australian Research Council and the ARCfunded Environmental Futures Network, and from the Wentworth Group of Concerned Scientists for MT to attend the XXXV Congress of the International Association of Hydrogeologists in Lisbon in September 2007.

The authors
Moya Tomlinson has a background in science communication and practical experience in water policy and planning with the Northern Territory government. She is currently completing an ARC-funded PhD at the University of New England assessing the environmental water requirements of a subterranean ecosystem, with a focus on ecological requirements of invertebrates in groundwaters and the ecosystem goods and services that they supply. Professor Andrew Boulton has worked on SGDEs since 1990, and has published papers on their ecological processes (for example, (Boulton et al. 1992, Boulton 1993, Boulton and Stanley 1996, Boulton et al. 1998, Boulton and Hancock 2006), Boulton et al. 2002) and goods and services ((Boulton 2000a, Boulton et al. 2003, Boulton 2005), Boulton et al. 2008) as well as presented invited addresses on SGDEs and processes threatening their ecology (SIL, Dublin 1998, Fenner conference 2001). He has been on several expert panels assessing ecological demands for SGDEs in Western Australia, South Australia, NSW and Queensland, and had considerable input into the NSW GDE policy document. He has co­ written two textbooks and over 100 research papers on aquatic ecology, and is internationally known for his work on GDEs, especially river baseflow systems and the hyporheic zone.



Executive summary

This Waterlines report is part of a series of papers commissioned on issues relating to Australian aquatic ecosystems. These Waterlines reports will contribute to improved environmental water management by stimulating discussion, synthesising current thinking, identifying knowledge gaps and highlighting areas that warrant further investigation. The papers draw together and synthesise the current knowledge and thinking on topics to stimulate ongoing discussion, debate and learning, highlight areas for further work, and improve general knowledge and understanding of the environmental water requirements. In some cases, guidelines and frameworks have been proposed to assist policy makers, planners and water managers in considering the issues. A part of each paper is the identification of whether further work would be beneficial in each area, and where these are identified, suggest directions for future investment. This project aimed to: • • review knowledge of the biodiversity, ecological processes and ecosystem services of subsurface groundwater dependent ecosystems (SGDEs) in Australia identify research directions that will provide accessible information and tools to help environmental water managers make informed contributions to the water planning process in relation to the needs of SGDEs in Australia.

We suggest that the sequestered location of SGDEs underground has led not only to these habitats being overlooked in favour of more accessible GDEs, but has also masked their diversity, ecosystem services and the close interconnections between SGDEs and other ecosystems. Recognition of the variety of subsurface groundwater habitats and of the key habitat characteristics of living space and resource supply will aid understanding of the drivers of SGDE ecology and the ecological significance of SGDEs. To assist this understanding, we outline a proposed typology of SGDEs that reflects a more ecologically-relevant scale for management than the current groundwater management unit does. Our overview of the biodiversity in SGDEs identifies extensive gaps in our knowledge of the distribution, composition and biodiversity value of Australian stygofauna (groundwater animals). Despite this incomplete inventory, it is apparent that stygofauna are present across a variety of Australian subsurface environments and are generally characterised by high diversity and local-scale endemicity. They are also often of high scientific interest, for example, the occurrence of the only known southern hemisphere representatives of several phyletic relict lineages. Microbes are a key component of SGDEs, forming the basis of the food chain and mediating the metabolism of carbon and other nutrients. Microbial activity degrades contaminants and delivers energy and nutrients to aquifer food webs and to biota in connected ecosystems. Microbially-mediated bioremediation and metabolism are examples of ecosystem services provided by SGDEs. Other goods and services include providing water for a range of consumptive uses, regulating the effects of floods, supplying ecological and evolutionary refugia, supporting other groundwater dependent ecosystems, and serving cultural values including those of science, Indigenous culture and recreation. The interconnections between SGDEs and other ecosystems, both terrestrial and aquatic (including marine), indicate that threatening processes in SGDEs typically threaten ecosystems connected to SGDEs. Anthropogenic disturbance (for example, pollution or overextraction) or management interventions either in SGDEs or their connected systems have flow-on effects, often with time lags, so that impacts might not be evident for decades. Disturbances to the groundwater regime result in a range of threats, including salinisation, pollution, eutrophication and land



subsidence. We give some examples of these in this review, and we also consider the likely impact of climate change on SGDEs in Australia. The interconnections between surface and subsurface ecosystems demonstrate that the water needs of SGDEs must be considered in truly holistic water planning; and ecosystem functions of SGDEs must be maintained if only to meet desired environmental outcomes for some surface waters. The National Water Quality Management Strategy guidelines (ANZECC/ARMCANZ 2000) state in Box 1.1 on page 2 of the Introduction that ‘groundwater should be managed in such a way that when it comes to the surface, whether from natural seepages or from bores, it will not cause the established water quality objectives for these waters to be exceeded, nor compromise their designated environmental values’ and that ‘little is known of the lifecycles and environmental requirements of [underground aquatic ecosystems and their novel fauna], and given their high conservation value, the groundwater upon which they depend should be given the highest level of protection’. National water reforms outlined in the National Water Initiative (NWI) require that water plans include an environmental allocation for the purpose of meeting environmental objectives, which are defined as maintaining ecosystem function (for example, through periodic inundation of floodplain wetlands), biodiversity, water quality; and river health targets. In its first assessment of jurisdictional implementation of the NWI, the National Water Commission found that progress towards environmental management of groundwater had not been achieved as envisaged. This lack of progress is unsurprising given the knowledge, technical and policy gaps identified in this review. We argue there is an overriding imperative for groundwater management to undergo a paradigm shift, even though there are uncertainties about the distribution, taxonomy and ecology of groundwater fauna, a lack of standard sampling protocols, no coordinated national recording of survey data, and no established tools for assessing SGDE ecological condition or predicting the magnitude and direction of change in condition following disturbance. The tools and techniques that will enable water managers to achieve NWI objectives can best be developed by research and management that take an ecological perspective. This means investigating key differences in habitat and resource supply between SGDE types, acknowledging the scale at which ecological processes occur, taking account of linkages between SGDEs and other ecosystems, and managing SGDEs on a scale that is informed by this ecological understanding. The European experience of integrating management of surface water and groundwater through the Water Framework Directive provides useful examples that merit closer attention in Australia. There are actions that can be taken without delay to improve cross-disciplinary working, take maximum benefit from existing data and knowledge, and target research effort most productively. The key research directions are: • • • more precise identification of SGDE types as a framework for investigations of ecosystem responses to disturbance in the groundwater regime confirmation that stygofauna provide useful indicators of the condition of SGDEs, and if they are determination of the level of taxonomic identification required for faunal indicators of ecosystem condition.

Progress in these inquiries will help identify priorities for management action, and also generate tools for water managers, so that knowledge and policy translates into water management arrangements that meet policy goals.



1 Introduction
1.1 Aims and scope of this review
The purpose of this review is twofold. Firstly, we summarise what is known about biodiversity in groundwater, the ecological processes in groundwater environments, and the ecosystem goods and services provided by subsurface groundwater dependent ecosystems (SGDEs). The focus is on Australia. Secondly, we match current knowledge with the knowledge needs of national policy on the environmental management of groundwater and its associated surface waters. From the gaps between existing knowledge and knowledge needs, we identify directions for research that will produce accessible information and tools to help environmental water managers to make informed contributions to the water planning process regarding the needs of SGDEs. The three main subject areas of this review – (1) biodiversity and taxonomy, (2) ecological processes and (3) ecosystem goods and services – are presented with reference to likely habitat types based on factors that influence subsurface biota and ecological processes (Figure 1). Figure 1: Conceptual model of factors influencing the biotic composition of SGDEs
History of natural and anthropogenic disturbance





Rate and volume of recharge

Aquifer material

rate and volume of infiltration



Groundwater regime: flux/flow, level/pressure and water quality gradients of environmental conditions Biogeography, life history strategies, biotic interactions Abundance, richness and distribution of subsurface fauna and microbes

Useable void space

Notes: This diagram is taken from and modified substantially from a diagram of variables known to influence the hyporheos (Brunke and Gonser, 1997)



1.2 What are SGDEs?
The need for careful definition
Our collective understanding of the ecology of SGDEs has lagged severely behind that of surface waters; this has hampered effective management. An equal hindrance to sustainable management of SGDEs is that the paradigm shift required for groundwater managers to fully embrace ecological principles such as ecological sustainability and resilience/resistance to disturbance has only just begun. Integral to such a paradigm shift is the consideration of new understandings of key concepts and agreement on conceptual models to encapsulate these definitions and convey a shared understanding and knowledge structure (after Benda et al. 2002). The concepts and definitions of hydrogeology ably serve the purpose of managing underground water for consumptive use. This goal of hydrogeology is demonstrated in the accepted disciplinary definitions of its basic materials: • • groundwater is all water beneath the watertable in soils and geologic formations that are fully saturated (Freeze and Cherry 1979) an aquifer is a geologic unit that can store and transmit water at rates fast enough to supply reasonable amounts of water to wells (bores) (Fetter 2001).

From an ecological point of view, these definitions are inadequate for sustainable management of groundwater. Ecology is the study of the relationships between living things and their environment. Ecologists study processes and interactions between and among the living and inanimate components of ecosystems. From an ecological point of view, it is not useful to designate water as groundwater simply on the basis of its subsurface location. Consider the case of a stream soon after draining into a cave in a karstic area. Although it is now technically groundwater, as it stands in a pool at the cave entrance, and as it flows through subsurface conduits and voids, it retains the physical and chemical characteristics of the surface stream for varying periods of time depending on rate of flow, interactions with the substrate or subsurface matrix, and degree of mixing with water from subsurface sources. Another example is a subsurface stream reach below large boulders and root mats (Collins et al. 2007) in which the biota and water chemistry (temperature, specific conductivity, dissolved oxygen, and dissolved organic carbon concentrations) of subsurface water are similar to those of the surface water. Similarly in the hyporheic zone – the zone of mixing between surface and groundwater below the bed of a stream (White 1993) – water is considered to be advected surface water until it undergoes physico-chemical changes due to interactions with groundwater and the sediment matrix (Fraser and Williams 1998). Groundwater is defined as water that has not yet been influenced by channel processes (White 1993). From an ecological perspective, aquifers are not simply containers of accessible and useable water: the flow of water towards a bore in economically useful amounts is not always ecologically meaningful. An ecological definition of an aquifer should consider its habitat characteristics: availability of food, shelter, and suitable conditions for respiration, reproduction and dispersal; and the accompanying biogeochemical transformations of energy and matter (compare this with the identification of streams as ecosystems by Triska et al. (1989)). An ecological perspective is apparent in the definition of an aquifer in the European Water Framework Directive (see later). This European definition requires two criteria to be considered in determining whether geological strata qualify as aquifers: (1) a significant flow of groundwater, and (2) that removal of groundwater would result in a significant diminution in the ecological quality of a surface water body or a directly dependent terrestrial ecosystem (Scheidleder et al. 2008). These ecological considerations frame our treatment of SGDEs, and point to the need for a functional definition of groundwater for this review (Box 1).



Box 1: A functional definition of groundwater Water that has been present in pores and cracks of the saturated zone of soil or rock for sufficient time to undergo physical and chemical changes resulting from interactions with the aquifer environment. This functional definition extends the hydrogeological definition (all water beneath the watertable in soils and geologic formations that are fully saturated) to one that is ecologically relevant. It is not proposed as a replacement for other definitions of groundwater, but it is suggested to help promote an ecological perspective. The temporal component of this ecological definition of groundwater recognises the role that changes in water chemistry play in determining the characteristics and function of groundwater. These physical and chemical changes have likely repercussions for subsurface microbes and invertebrates as well as for human consumption of groundwater. The growing recognition that groundwaters are integral to many surface water systems and are ecosystems in their own right is reflected in at least two decades’ awareness of groundwater dependent ecosystems (GDEs), largely initiated in Australia by Hatton and Evans (1998). These authors identified four main types of GDEs: terrestrial vegetation, river base flow systems, aquifer and cave systems, and wetlands. The degree of dependency of these ecosystems on groundwater varies from complete dependency in the case of aquifer ecosystems, to opportunistic use of groundwater by some terrestrial vegetation. SKM (2001) extended their consideration of ecosystem dependency to include two more types – terrestrial fauna, and estuarine and nearshore marine systems. They also suggested three key attributes of groundwater on which ecosystem dependency is based (Box 2). Box 2: Attributes of the groundwater water regime (GWR) (SKM 2001) • • • flow or flux, or the rate and volume of supply of groundwater water level in unconfined aquifers and pressure in confined aquifers the chemical quality of groundwater expressed in terms of pH, salinity and/or other potential constituents, including nutrients and contaminants.

The attributes on which ecosystem dependency is based comprise the environmental water requirements of that ecosystem. Changes in these attributes could be deleterious to dependent ecosystems. For example, reduced groundwater flow can affect the rate of discharge to dependent ecosystems such as cave or estuarine environments; lowered water levels can fall below the rooting depth of groundwater-dependent terrestrial vegetation; and changes in water quality can exceed the tolerance ranges of aquifer fauna. Most recently, Eamus et al. (2006) grouped GDEs into three classes (Box 3): Box 3: Classes of GDE (Eamus et al. 2006) • • • aquifer and cave ecosystems ecosystems dependent on the surface expression of groundwater, for example mound springs, baseflow rivers, and estuarine seagrass beds ecosystems dependent on the subsurface presence of groundwater, for example where vegetation has roots accessing groundwater.

This classification identified ecosystems associated with a common groundwater resource. Its purpose was to assist managers to identify appropriate tools for assessing groundwater dependency; for example, for the first class, microbial plating or faunal sampling; for the second, stable isotopes or tracers; and for the third, physiological measurements of plant water use. The advantage of this classification is that it goes some way towards helping us seek parallels and contrasts in the behaviour of functionally-similar GDEs.



This review focuses on aquifer ecosystems, here termed SGDEs (Box 4), and the aquatic fauna that inhabits these ecosystems. Box 4: Subsurface groundwater dependent ecosystem An 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 groundwater supply. Adapted from Parsons and Wentzel (2007) These systems are the least known GDEs, partly because of their sequestered nature, but also because research into terrestrial GDEs has been prioritised following the recommendation of Hatton and Evans (1998) that there not be a large investment in investigations of aquifer ecosystems. Subsequent research has focused on the water needs of terrestrial GDEs, and a recent ‘toolbox’ of techniques (Clifton et al. 2007) for assessing the environmental water requirements of GDEs addresses only terrestrial vegetation, wetlands and river systems. Despite the shared characteristic of being subterranean, there is a great variety of aquifer systems in karstic, calcrete, alluvial and fractured rock environments. Not all subterranean ecosystems and species are groundwater dependent. Caves and other subsurface voids can harbour terrestrial fauna (troglofauna (Humphreys 2000a)) that do not rely directly on groundwater, although groundwater provides a humid environment and carries food from the surface. Troglofauna have been recorded from caves in karstified carbonate rocks in the Kimberley, Cape Range, Barrow Island, Perth Basin (for example, Eneabba, Jurien, Yanchep), the Leeuwin-Naturaliste Ridge and the Nullarbor Plain (Eberhard 2007) and in voids of pisolite in the Pilbara (Biota Environmental Services 2006). Figure 2 shows regions and places mentioned in this report. Due to their dependence on high relative humidity, troglofauna might be affected by aquifer dewatering and other changes to the groundwater regime and so could have some groundwater dependence. Where terrestrial fauna are found in association with particular groundwater habitats, such as fauna on cave walls permanently wetted by seeping groundwater (Sket 2004), they are clearly groundwater dependent. For example, Sket (2004) describes leptodirine beetles in the film of seeping groundwater on the walls of karstic caves from north-eastern Italy to Montenegro. These beetles walk in the film, dipping their mouthparts into the water to collect food particles. Their morphological adaptations to this environment include thickened femora, large, curved claws, and mouthparts specialised for filter feeding. Anchialine habitats illustrate the variety and complexity of many SGDEs. These habitats are bodies of saline water with subterranean connections to the sea and restricted openings to the open air, showing marine and terrestrial influences (Iliffe 2000). Anchialine pools and sinkholes are stratified, with fresher groundwater overlying deeper saline water. Water in anchialine pools or sinkholes reflects tidal movements to a varying extent, depending on distance from the sea. Typically, anchialine fauna occur at depths where the salinity is equivalent to that of seawater (Humphreys 1999b).



Figure 2: Location of regions and places referred to in this report

Christmas Island (2300 km NW of Perth) Kimberley Barrow Island Pilbara Cape Range Murchison region Alice Springs Great Artesian Basin Ngalia Basin

Nullarbor Yanchep Perth LeeuwinNaturaliste ridge Yilgarn Peel alluvium

Jewel Cave

1.3 Brief description of the main occurrences of SGDEs
Unconsolidated aquifers
Unconsolidated aquifers consist of particles of gravel, sand, silt or clay that are not bound by mineral cement, by pressure or by thermal alteration of the grains (Freeze and Cherry 1979). Deposition can be by wind (aeolian aquifers, for example in sand dunes), flowing water (alluvial aquifers), or by settlement of sediment in lakes (lacustrine aquifers). Stanford and Ward (1993) proposed that alluvial aquifers are a component of a continuum in which the aquifer-river complex can be conceptualised as a network of active channels and a series of hydrogeological units linked dynamically by the ‘hyporheic corridor’. Zones and pathways of differential permeability follow palaeochannels laid down by variable flows. On a larger scale, alluvial aquifers represent an interstitial highway linking spatially discontinuous subterranean ecosystems with surface waters (Ward and Palmer 1994). Stygofaunal surveys have concentrated on unconsolidated alluvial habitats because these high-yielding aquifers are the focus of groundwater extraction and the associated network of monitoring bores allows ready access for sampling (Hancock and Boulton in press).

Fractured rock aquifers
Fractured rock aquifers occur in rocks of sedimentary, igneous or metamorphic origin. Fissures or cracks develop along bedding planes or in zones of stress caused by pressure changes due to tectonic movement, glaciation, erosion of overburden, or rapid temperature changes (Fetter 2001).



Groundwater flow follows the fractures, but in sedimentary rock, the flow might also permeate the rock matrix: depending on the geology there can be a complex and spatially variable dualporosity environment. Fissures and joints can become enlarged solution cavities that eventually form large voids. Fractured rock aquifers are undersampled, but stygofauna have been recorded from this habitat type in the Pilbara region of Australia (Eberhard et al. 2005).

Karst is a term describing a landscape rather than an aquifer type (Fetter 2001). It is a terrain characterised by sinkholes, caves and springs developed most commonly in carbonate rocks where significant solution of the rock has occurred due to flowing water. The distinct landforms of karst are due to the action of subterranean drainage. Karstic terrain can also develop by other processes – weathering, hydraulic action, tectonic movements, melt water and the evacuation of molten rock (lava). Because the dominant process in these cases is not solution, this suite of landforms is termed pseudokarst (Halliday 2007). An example is the Undara Lava Tubes in north Queensland. Karst in Australia occurs in scattered outcrops in the highlands from north Queensland to Tasmania, with a concentration in south-east Australia; in dunal limestones along south westerly facing shores from Cape Range, Western Australia to Victoria; extensively in marine limestones on the Nullarbor; in the Kimberley, and across northern Australia to the Barkly Tableland in Queensland (Finlayson and Hamilton-Smith 2003). The karstic caves in the Swan Coastal Plain and the Leeuwin-Naturaliste Ridge contain root mat communities (Jasinska et al. 1996), which are listed as threatened ecological communities under Commonwealth endangered species legislation (see later section). Karstic systems provide a wide variety of habitats characterised by periodicity of saturation, climatic influences and degrees of connection to streams and groundwater systems. They are also highly heterogeneous due to spatial differences in groundwater flow rates because of the variable occurrence of conduits and fissures (Bakalowicz 2005).

Calcrete aquifers
Calcretes are carbonate deposits that form in the soil or in the vicinity of the watertable as a result of evaporation of soil water or groundwater respectively. Calcretes may develop along palaeochannel systems in a succession of chemical precipitations associated with increasing salinity. Episodic recharge and fluctuating groundwater levels create solution cavities along low-gradient drainage lines. Calcrete aquifers are technically karstic because the cavities are formed by solution, but it is useful to treat them here as a separate habitat type. Groundwater calcretes (Mann and Horowitz 1979) occur in Australia north of about latitude 30° South in an area where mean annual rainfall is less than 200 millimetres and potential annual evaporation exceeds 3000 millimetres. These provided refugia for relict lineages following the onset of aridity (Humphreys 2001). Calcrete aquifers are widespread in the Australian arid zone and many of those already sampled have yielded a rich and diverse invertebrate fauna (Humphreys 2001, Watts and Humphreys 2006) in which the species are largely endemic to a single calcrete body (Leys et al. 2003, Cooper et al. in press, Guzik et al. 2008).

Another type of chemically-precipitated aquifer occurs in pisolote mesas or channel iron deposits in the Pilbara. These are highly permeable due to tertiary porosity and are a potentially rich but little investigated faunal habitat (Biota Environmental Services 2006).



Ecotones: the hyporheic and vadose zones
The definition of groundwater ecosystems has broadened to include the hyporheic zone (Hancock et al. 2005). The hyporheic zone is the zone in a stream bed where surface water and groundwater mix (White 1993). It can be defined more specifically as ‘a spatially fluctuating ecotone between the surface stream and the deep groundwater where important ecological processes and their requirements and products are influenced at a number of scales by water movement, permeability, substrate particle size, resident biota, and the physicochemical features of the overlying stream and adjacent aquifers’ (Boulton et al. 1998). Upwelling groundwater creates zones of low dissolved oxygen and organic matter, the very conditions favourable to stygobites. In the arid zone, the hyporheos of ephemeral streams is groundwater-dependent for most of the time, many species relying entirely on subsurface water after surface pools have dried (Boulton et al. 1992, Cooling and Boulton 1993). The vadose zone is the unsaturated zone above the watertable in which the spaces between particles are only partially filled with water. Water in the vadose zone can be percolating rainwater or discharging groundwater. In the arid zone, where rainfall is low but groundwater tables are close enough to the surface to support terrestrial vegetation (O'Grady et al. 2006a), 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 or ‘skin of karst’ (Bakalowicz 2004). The epikarst in Europe (Pipan and Culver 2007) and North America (Pipan et al. 2006) has been found to hold a diverse stygofauna distinct from the fauna found in the saturated zone. Sampling of epikarst in southwestern Western Australia, Tasmania and New South Wales indicates that epikarst is likely to support stygofauna (Eberhard 2004).

Another largely uninvestigated subterranean habitat can be found in aquitards, or compact aquifers (after Hahn and Fuchs (submitted)) comprising aquifers with a reduced pore size and a very low hydraulic conductivity (less than 10–6 m/s), such as clay, loess and very fine sands, and also compact rock formations. A survey of 16 bores (sampled twice) in ‘compact aquifers’ in Germany yielded stygofauna in more than half of the bores, although the fauna was depauperate compared with that of nearby alluvial, karstic and fractured rock aquifers. These compact formations, which are not technically classified as aquifers, are SGDEs and might play a role in the resilience of other groundwater ecosystems (Box 5), for example by contributing to habitat heterogeneity. We are not suggesting here that each of these habitat types necessarily harbours a distinctive fauna. Where connections between habitats exist, there might be a broad overlap of taxa, although richness and abundances differ. Eberhard et al. (2005) state that, with the exception of large taxa such as fish, which require large voids and are restricted to karstic aquifers, stygofauna from the Pilbara and adjacent areas are found wherever groundwater environments provide suitable habitat, including in porous, karstic, and fractured-rock aquifers as well as the hyporheic zone and springs.

Box 5: Resistance and resilience Resistance is the capacity to withstand a disturbance, for example through desiccationresistant eggs or life stages. Resilience is the ability to recover from a disturbance, for example, by occupying refugia offered by fine scale microhabitat differences. (Fritz and Dodds 2004)



This tendency to habitat generality by many taxa indicates that conclusions about habitat affinity and consequent faunal distribution based on limited sampling should be drawn with caution. But it is also true that some taxa are restricted in range, sometimes to within a single calcrete body (Cooper et al. in press). Rather than enabling prediction of faunal distribution, the suggested habitat types offers an approach to understanding the main aspects of groundwater regime and living space, the habitat traits most relevant to stygofaunal community composition. These habitat aspects are likely to be hierarchically important, 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.

1.4 A fundamental property of SGDEs: connection to other ecosystems
SGDEs are 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 (Figure 3). There can also be direct connections between SGDEs, for example, where an alluvial aquifer overlies or is interdigitated with another aquifer type. The interfaces between habitats are usually characterised by spatially and temporally dynamic gradients in environmental conditions that make precise delineation of ecosystem boundaries difficult. 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 interconnections between SGDEs and surface aquatic systems are most well-known in alluvial aquifers that are hydraulically interactive with rivers and floodplains over extensive reaches. In these environments, the hyporheic zone often extends not only longitudinally along the river but also laterally for several kilometres, suggesting that alluvial aquifers can be conceptualised as the core of an ‘interstitial highway’ (Ward and Palmer 1994).

Figure 3: SGDEs (centre) are linked through ecotones (speckled area) to other ecosystems (outer circle)

Terrestrial vegetation Vadose zone

Riparian vegetation Freshwater psammolittoral

Marine psammo littoral Marine and estuarine Hyporheic zone Marine upwelling and intrusion Surface waters (Springs, rivers, wetlands)



1.5 Characteristics of SGDEs and their fauna
Despite the variety of SGDEs, there are parallels in the contrasts between lightless subsurface environments and those of most surface environments (see Table 1). Table 1: Characteristics of groundwater environments and implications for groundwater biodiversity and ecology
Characteristics of groundwater environments Implications for fauna Implications for biodiversity, ecological processes and ecosystem services

Relatively stable environmental conditions compared with surface aquatic environments

Buffering from environmental change taking place at the surface Fauna are morphologically conservative Selective pressure towards delayed breeding, longer life cycles, larger size and fewer young Reduced habitat heterogeneity (Sket 1999)

Persistent habitat for relict lineages Fauna are potentially vulnerable to changes in groundwater regime Morphological similarity and cryptic speciation requires that taxonomic approaches combine morphological and molecular investigations


No primary producers; herbivores represented only by root-mat feeders; fewer predators; a trophic shift towards omnivory; food web truncated and dominated by detritivores (Gibert and Deharveng 2002)

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 roles in supporting biodiversity and ecosystem function Some species have restricted ability to respond rapidly to environmental change or to recolonise readily after local extinction; low resilience and resistance Some species are able to respond rapidly to prolonged increases in food availability Close monitoring is required to detect population decline but response time can be decades

Typically restricted inputs of energy; low productivity

Fauna have slower metabolic rates (Danielopol et al. 1994), longer life cycles, lower fecundity (Dole-Olivier et al. 2000) than surface counterparts Overall densities are usually very low due to lack of food

May be spatially discrete or patchy

Restricted dispersal and recruitment

High potential for speciation and short range endemism Vulnerable to habitat change resulting in local or total extinction of species



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 ecosystem services provided by SGDEs. Heterotrophy rather than photosynthesis is the basis of the food chain (Gibert and Deharveng 2002), and it is largely carried out by biofilms coating surfaces and sediment particles. Biofilms are consortia of bacteria and fungi in a mucilaginous polysaccharide matrix secreted by the microorganisms (Brunke and Gonser 1997, Mauclaire et al. 2000). Primary producers are not entirely absent from aquifers, although lightlessness precludes photosynthesis; Kuehn et al. (1992) document 21 species of soil algae in groundwater associated with recharge zones, and suggest that algal populations are likely to supplement the diet of aquifer fauna. Ellis et al. (1998) recorded 24 genera of algae some four kilometres from the river in a highly transmissive alluvial aquifer. Groundwater environments are dynamic systems in which biological and geochemical interactions and transformations take place at a range of scales. Shifting patterns of physico­ chemical, oxygen and nutrient gradients (see later) create a patchy mosaic of microenvironments (Pospisil 1994, Coineau 2000) constituting a set of functional mesohabitats that can be distinguished by hydraulic and physical characteristics (Brunke et al. 2001). Absence of light and widespread perceptions of reduced habitat heterogeneity, low productivity, and unfavourable but stable and predictable environmental conditions belie the true diversity of aquifer habitats and the habitat differences that are key to appreciating the subtle complexities of subterranean ecology. Features of ecological relevance in particular aquifers could be small-scale exchange processes between surface and groundwater (Sophocleous 2002), and patchily-occurring patterns of recharge, or zones of higher transmissivity due to palaeochannels (Ward et al. 1994), which drive spatial and temporal variability in biogeochemical processes and faunal distribution, abundance and richness. An ecological perspective that recognises these small-scale differences within habitats, as well as the differences between habitat types, is more likely to identify knowledge gaps that translate into carefully planned and targeted research questions.

1.6 Drivers of groundwater ecology
Dissolved oxygen is a key environmental parameter in interstitial environments (Danielopol et al. 1994, Ward et al. 1998), although Malard and Hervant (1999) state that dissolved oxygen is not a limiting resource for all animals in groundwater, as faunal distribution in many studies does not match oxygen gradients, and further, not all groundwater habitats have low dissolved oxygen. However, Hahn (2006) found oxygen concentrations of one milligram per litre to be a critical limit for subsurface fauna. Although a correlation between an easily-measured variable, such as dissolved oxygen, and a measure of community condition, such as species richness, would be ideal for the purpose of management, such a relationship is seldom apparent or consistent. Some studies show weak correlations between individual water quality variables and stygofaunal community composition or species distribution (Dumas et al. 2001, Hahn 2006, Castellarini et al. 2007b). Others show contrasting results. For example, Mauclaire et al. (2000), working in a glaciofluvial aquifer some 20 kilometres east of Lyon, France, found that, while bacterial activity and abundance were correlated with dissolved organic carbon (DOC) concentrations, faunal abundance was relatively homogeneous and only weakly correlated with DOC. However, in the same aquifer, but at sites closer to the Rhône River, Datry et al. (2005) reported that groundwater invertebrate assemblages were more abundant and diverse in sites artificially recharged with storm water compared with reference sites recharged by rainfall infiltration. Concentrations of dissolved organic carbon (DOC) were significantly higher in the recharge sites than in reference sites, where the thickness of the vadose zone was less than



10 metres in all sites, although mean concentrations of DOC were no greater than one milligram per litre at any site. In contrast, Masciopinto et al. (2006) reported that, in wells affected by artificial recharge of waste water in southern Italy, increased DOC at similar concentrations to the Datry study was associated with a decline in faunal biodiversity. DOC concentration in bedrock zone groundwater is typically quite low; Wetzel (2001) cites a median DOC content of groundwater as 0.65 milligrams per litre. This is comparable to a median value of 0.7 milligrams per litre recorded in a survey of 100 bores and springs in 27 states of the US (Kaplan and Newbold 2000). These results might indicate differences in the quality rather than quantity of DOC (Sobczak and Findlay 2002). The bioavailability of DOC varies, and depends on its source and chemical composition. DOC consists of an extremely complex mix of organic compounds of varying structure and molecular weight. The more labile, simpler compounds are metabolized more rapidly by bacteria, although there is some evidence that more complex compounds support higher bacterial numbers over longer time periods (McDonald et al. 2007). Although organic matter supply may be necessary to sustain life, species richness, faunal community composition and spatial patterning are likely to be determined by multiple interacting factors: transmissivity, oxygen, dissolved organic carbon, redox and pH accounted for 52 per cent of the variability in faunal abundance in two French alluvial riverbank aquifers (Mauclaire and Gibert 2001). The conflicting results could also be due to the limitations of measuring water quality variables from pumped groundwater in which mixing effects mask small-scale heterogeneity in aquifer conditions (Strayer 1994). Physico-chemical variables are also unlikely to be the sole determinants of species distributions and community assemblages. Dispersal constraints (Belyea and Lancaster 1999), such as hydrological disconnection (Sheldon and Thoms 2006), could isolate parent populations from which populations observed at any particular sampling time are derived. Lag effects are likely, so that the species presence and abundance data collected at any sampling time could result from previous rather than current physico-chemical conditions. There might also be multiple points of population or community stability due to varying influences of different combinations of driving variables as environmental conditions change.



2 Biodiversity values of SGDEs
2.1 Defining biodiversity
The Convention of Biological Diversity (1992) defined biodiversity as ‘the variability among living organisms from all sources, including terrestrial, marine and other aquatic ecosystems, and the ecological complexes of which they are part; this includes diversity within species, between species and of ecosystems’. Biodiversity thus has genetic, species, community and landscape components, all of which relate to each other and should not be considered in isolation. The spatial components of biodiversity at the species level can be differentiated as the number of species at a location, the number of species in the regional species pool, and the variability in numbers of species between localities within a region (Thompson and Starzomski 2007). Thus the biodiversity of SGDEs encompasses both the fauna and the habitats. The term biodiversity ‘hotspot’ is commonly used to denote areas with high species richness and endemism (Reid 1998), but it is defined more usefully for management by Myers et al. (2000) as ‘areas featuring exceptional concentrations of endemic species and experiencing exceptional loss of habitat’. The term was applied arbitrarily by Culver and Sket (2000) to cave and karst well sites with 20 or more obligate subterranean species of troglofauna or stygofauna. Using this criterion, many Australian sites would qualify as hotspots. For example, one bore in the Pilbara has yielded at least 32 stygobitic taxa (Eberhard et al. in press).

2.2 The value of biodiversity
Biodiversity conservation serves a number of values (Box 6). Box 6: Values served by biodiversity conservation • • • • • preservation of genetic diversity and therefore of species’ ability to adapt to environmental change protection of threatened species or ecosystems maintenance of ecosystem functions such as provision of goods and services maintenance of ecosystem resistance and resilience, or the ability to resist or recover from disturbance intangible human social and cultural benefits.

(Thompson and Starzomski 2007) It is a social and political decision whether these values justify conservation action; for example, does the protection of a ‘tiny, blind cannibal’ take precedence over the mining of $12.5 billion of iron ore (see The West Australian, 30 March 2007)? Prioritisation of these values is usually implicit rather than explicit in biodiversity management. Funds could be allocated more readily for the protection of rare and endemic fauna than to a community of microbes, yet the loss of ecosystem services not only has economic repercussions but could be accompanied by a greater loss of biodiversity.



2.3 Subterranean biodiversity
Patterns of subterranean biodiversity are the product of four particular characteristics (Gibert and Deharveng 2002): • • • low number of lineages due to the ecological filter of the transition to lightless environments high endemism due to fragmentation of habitat high level of relict taxa due to persistence of environmental conditions over long geological periods of unfavourable surface conditions, for example during the onset of aridity truncated food webs with few predators and herbivores and no primary producers. The absence or reduction in importance of predators is a result of a shift towards omnivory imposed by scarcity or irregularity of food supply.

Terminology for subterranean fauna varies in the literature. An initial distinction can be made between aquatic and terrestrial subterranean fauna, termed stygofauna and troglofauna respectively. Although collectively termed stygofauna (Hancock et al. 2005), groundwater species are often classified according to their affinity to groundwater habitats (Gibert et al. 1994) (Figure 4). Figure 4: A classification of groundwater species based on their affinity to groundwater habitats

Surface water

life cycle


Species can be (a) stygoxene, accidentally or facultatively present in groundwater habitats (b) stygophile, completing part of the life cycle in groundwater habitats (c) stygobite, obligate inhabitants of groundwater habitats throughout the life cycle. Adapted from Gibert et al. (1994)


Species that complete their entire life cycles in groundwater and are seldom found in surface waters are termed stygobites. In spring discharge sites and in alluvial aquifers with strong hydrological connections to surface water bodies, there could be stygophilic species that spend part of their life cycle in groundwater, and stygoxenes, species that are accidental or facultative visitors to groundwater habitats. In parallel terminology for the hyporheos (the fauna of the hyporheic zone) Williams and Hynes (1974) distinguished the occasional hyporheos, taxa that spend part of their life cycles in the hyporheic zone, from the permanent hyporheos, taxa that complete their life cycles in the hyporheic zone. The trap for the unwary reader is that, in some groundwater habitats, the entire stygofaunal assemblage will be stygobitic, but in others will variously comprise stygobites, stygophiles and stygoxenes. Readers should be aware of differences in usage of the term stygofauna for groundwater fauna in caves and karsts (Thurgate et al. 2001), alluvial (Dole-Olivier et al. 1993) or calcrete (Watts and Humphreys 2006) aquifers, or an array of groundwater environments both subsurface and surface (Eberhard et al. 2005). In this review, we use the



term stygofauna to encompass all groundwater fauna, but where necessary, use the classification by Gibert et al. (1994) to distinguish stygoxenes, stygophiles, and stygobites.

2.4 Characteristics of stygobitic fauna
Obligate groundwater invertebrates have morphological, physiological, behavioural and life history adaptations (Box 7). Morphological adaptations (Figure 5) include loss of pigmentation, small size, eye reduction or loss, elongate or attenuated body shape, and hypertrophy of some sensory organs, but development of sensory setae (Gibert et al. 1994). Physiological and behavioural adaptations to suboxia (dissolved oxygen concentration (DO) less than 3.0 milligrams per litre) or limited food supply (Malard and Hervant 1999, Hervant and Renault 2002, Datry et al. 2003) include lower energetic requirements compared with surface water forms; high storage of fermentable fuels, providing a more sustained supply for anaerobic metabolism; low metabolic rate in normoxia (DO less than 3.0 milligrams per litre) and a further reduction by reducing locomotion and ventilation in hypoxia (DO less than 0.01 milligrams per litre); and the ability to rapidly resynthesise glycogen stores during post­ hypoxic recovery. Box 7: Adaptations to subsurface groundwater habitats • • • • • • • • • • eye loss or reduction small size loss of pigmentation attenuated body shape development of sensory setae fewer but larger eggs longer time for egg development longer life cycles lower metabolic rates reduced locomotory and physiological activity in response to environmental stress.

(Gibert et al. 1994, Hervant et al. 1999, Eberhard 2005, Jarvis et al. 2005) These adaptations confer greater tolerance of starvation and low oxygen levels on stygobites compared with surface water fauna (Hervant et al. 1995, Hervant et al. 1999). The European groundwater amphipod Niphargus sp. survived for two months in hypoxic water, but a surface water amphipod Gammarus sp. survived for only two days (Danielopol 1989). Hypoxia is nevertheless a stressor for stygobites, and heavy nutrient contamination and subsequent oxygen depletion can result in high mortality (Sinton 1984). The higher tolerance of suboxia in stygobites might confer a competitive advantage over stygophilic taxa, but if oxygen supply is adequate in nutrient-enriched environments, the higher metabolic rates of stygophiles might enable these taxa to out-compete stygobites (Wilhelm et al. 2006). Danielopol et al. (1994) describes the subsurface isopod Proasellus slavus as euryoxic (tolerant of a wide range in oxygen concentration), but having a physiological optimum at higher oxygen concentrations. Oxygen availability can account for differences in interstitial faunal composition (Boulton et al. 1997, Marmonier et al. 2000). Redox gradients that influence local oxidation pathways are partly determined by porosity, which can influence entrainment of allochthonous organic matter (Gibert et al. 1994). Despite a tolerance of suboxia, fauna in unconfined aquifers preferentially occupy the zone just below the watertable where dissolved oxygen and nutrient concentrations are highest (Pospisil 1994, Edler and Dodds 1996, Sarkka and Makela 1999). Thus 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, indicate that small-bodied fauna such as copepods are able to follow declining water levels, or perhaps become entrained, but larger bodied species such as amphipods become stranded (Tomlinson et al. 2007b). Life history adaptations by stygofauna to the relatively more stable aquifer environment are summarised by Dole-Olivier et al. (2000). These include fewer but larger eggs; a longer time for egg development (Rouch and Danielopol 1999) and longer life cycles. For example the European amphipod Niphargus sp. lives 10 years (Mauclaire et al. 2000) and the isopod Stenasellus virei boui takes 10 years to develop from egg to adult (Rouch and Danielopol 1999), compared with a mean life span of six months for the benthic amphipod Gammarus chevreuxi (Subida et al. 2005). Figure 5: A new genus of bathynellid syncarid

This new genus of bathynellid syncarid illustrates morphological adaptations to the groundwater environment: small size, loss of eyes and pigment, attenuated body shape and development of sensory setae. Photo: Peter Hancock

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 so that European results may be extrapolated with confidence. These life history adaptations to the relatively stable aquifer environment would not be advantageous in a situation of environmental change such as anthropogenic water level fluctuations. Fauna in seasonally unfavourable or unpredictable environments either migrate or become dormant during adverse conditions (Gyllstrom and Hansson 2004). Dormancy is a state of suppressed development presenting as either quiescence (a short-term response to a limiting factor) or diapause (an obligate period of arrested development triggered by environmental factors) (Dahms 1995). Diapause in unfavourable environmental conditions is known for surface water species of taxa that include groundwater forms, for example, copepods (Hairston et al. 1995, Hairston and Caceres 1996) and tardigrades (Rebecchi et al. 2006), but has not yet been recorded in groundwater forms.

2.5 Australian stygobitic biodiversity
Table 2 summarises Australian stygobitic biodiversity as records of taxa in a variety of groundwater environments. Following Sket (1999), surface water taxa and inhabitants of wet soil were excluded. The groundwater environments are listed as reported in the literature, but are not mutually exclusive; for example calcrete aquifers might or might not be karstified, and calcrete deposits are often inter-fingered with alluvium resulting in heterogeneous environments.



Survey effort in Australia is patchy and incomplete; but it has rapidly improved in recent years, with many exploratory baseline surveys being conducted, particularly in Western Australia as part of the environmental impact assessment for mining developments. Existing survey work covers some coastal and inland alluvial, fractured rock and arid zone karstic and calcrete aquifers and caves in the Northern Territory, New South Wales, Queensland, Tasmania, Western Australia and Christmas Island. In Europe the number of endemic stygofauna is greater in karstic systems than in alluvial aquifers, perhaps because the greater isolation of karstic habitats facilitates speciation (Danielopol et al. 2000). Because much of eastern Australian karst is sparsely surveyed (Thurgate et al. 2001), it is likely that much stygobitic diversity remains undocumented. The apparent patterns of biodiversity probably reflect available taxonomic interest and expertise; unexplored groups could be equally diverse. Table 2: Stygobitic biodiversity in Australia
Taxa Protista Platyhelminthes Aschelminthes Turbellaria Nematoda Rotatoria Tardigrada Annelida Oligochaeta Polychaeta Mollusca Gastropoda Hydrobiidae Glacidorbidae Arachnida Crustacea Acarina Ostracoda Myodocopida Podocopida Halocyprida unidentified Copepoda Cyclopoida Harpacticoida Calanoida Misophrioida unidentified Remipedia Syncarida Nectiopoda Psamm­ aspididae Koonungidae Anaspidae Bathynellidae Para­ bathynellidae Undescribed family Decapoda Isopoda Atyidae Phreatoicidae Janiridae 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 Calcrete ? 9 ? Alluv -ial 9 9 9 Anchialine ? ? Karst: freshwater ? 9 ? Fractured rock ?



Taxa Flabellifera Tainisopidea Amphisopidae Oniscidea Cirolanidae Amphipoda Paramelitidae Neo-niphargidae Melitidae Bogidiellidae Hadziidae Crangonyctidae Chiltoniidae Spelaeo­ griphacea Thermos­ baenacea Insecta* Coleoptera Dytiscidae Elmidae Vertebrata Pisces

Calcrete 9 9

Alluv -ial


Karst: freshwater

Fractured rock


9 9

9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9

After Poore and Humphreys (1998), Humphreys (2000b, 2001), Jaume et al. (2001), Thurgate et al. (2001), Eberhard et al. (2005), Humphreys pers. comm., Humphreys (2006b), Pinder et al. (2006), Tomlinson, unpublished data). Ticks indicate a record for the taxon. Question marks indicate that occurrence is likely but unrecorded to date *Hyporheic fauna recorded from alluvial habitats in Australia also include stygophile taxa: – Coleoptera (Scirtidae); Diptera (Ceratopogonidae, Chironomidae, Muscidae, Simuliidae, Stratiomyidae); Ephemeroptera (Baetidae, Caenidae, Leptophlebiidae); Megaloptera (Corydalidae); Odonata; Plecoptera (Gripopterygidae); Trichoptera (Calamoceratidae, Calocidae, Ecnomidae, Hydrobiosidae, Hydroptilidae, Leptoceridae, Philopotamidae) – (see Cooling and Boulton 1993, Boulton and Foster 1998, Hancock 2006, Boulton et al. 2007).

Table 2 is incomplete and unsatisfactory for a number of reasons: much of Australia’s stygofaunal biodiversity remains unsurveyed, there is a serious lack of taxonomic capacity despite the efforts of the last decade (Humphreys 2008), much information is not readily accessible because it resides in consultancy or government reports and other grey literature or in individual researcher’s records; definitions of stygofauna are not always clear in the published literature, or the degree of groundwater dependency of the specimen was unknown to the authors, so that reported biodiversity variously includes stygobites, other taxa that use groundwater habitats for part of their lifecycle, or facultative visitors; reports of stygofaunal distribution do not always indicate the habitat type; and the records are sometimes incompatible because of taxonomic revision and re-assignment over time. These issues demonstrate the urgent need for a central register or database of stygofaunal taxa conforming to a standard, nationally-agreed terminology and including metadata such as sampling method, frequency of sampling, details of aquifer type and other location data, and associated details of water quality (for example, conductivity and dissolved oxygen). European groundwater faunal populations are dominated by crustaceans, with stygobitic species making up 40 per cent of the total European crustacean fauna (Danielopol et al. 2000). Crustaceans – including amphipods, copepods, ostracods and isopods – are also the majority of Australian stygofauna. Surveys to date, largely focused on Western Australia, have revealed a new genus of isopod (Wilson 2003), 41 species of copepod (Karanovic 2006) and over 110 species of ostracod (Reeves et al. 2007) in the Pilbara region alone, and 31



species of copepod from the Murchison area of the Yilgarn Craton (Karanovic 2004). Of the crustacean superorder Syncarida, anaspids are restricted to southern Australia (Hobbs 2000). The bathynellids are well-represented and largely undescribed, although the Western Australian fauna have received some attention (Cho 2005, Cho et al. 2005, Cho et al. 2006a, Cho et al. 2006b). A wide range of other taxa are represented in Australia, including more than 80 new species of dytiscid diving beetles (Watts and Humphreys 2006, Watts et al. 2007) and two species of fish (Humphreys 1999a). Priority groups for taxonomic work are the amphipods, isopods and bathynellids (Professor Andrew Austin, University of Adelaide and Dr. Steve Cooper, South Australian Museum, pers. comm.). The diversity of subsurface microbial (Kimura et al. 2005, Goldscheider et al. 2006), fungal and protozoan (Novarino et al. 1997, Ellis et al. 1998, Andrushchyshyn et al. 2007) communities is virtually unexplored in Australia. Some biochemically novel, chemoautrophic communities consisting of mucoid sheets or tongues and dependent on nitrite oxidation have been described from karst of the Nullarbor Plain (Holmes et al. 2001, Subterranean Ecology 2007). Characteristic of the Australian stygofauna are taxa that are relicts of ancient lineages and have very limited distributions. The anchialine fauna of Cape Range are an example of the persistence of phyletic relict fauna buffered from climatic and other environmental change. The Cape Range fauna are hypothesized to derive from populations that were already inhabiting subterranean habitats before the breakup of Gondwana (Humphreys 2000b). They include 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 only four globally) from the Fortescue valley in the Pilbara (Poore and Humphreys 1998, 2003). Harvey (2002) defined short-range endemic species as those with a range of less than 10,000 square kilometres, and noted that the majority of short-range endemic species possess characteristics such as limited dispersal ability and confinement to discontinuous habitats. Eberhard et al. (in press) suggested that 1000 square kilometres may be a more satisfactory threshold for short-range endemism. The high diversity of short-range endemic dytiscid diving beetles in calcrete aquifers in the Pilbara has been ascribed 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), oniscidean isopods (Cooper et al. in press) and parabathynellids (Guzik et al. 2008) from these calcretes support this interpretation.



3 Subsurface ecological processes

Energy – the capacity to do work – is ultimately derived from the sun. It flows through food webs as chemical bonds in organic compounds, and it is dissipated through respiration or stored in sediments. Chemical elements cycle through organisms and their abiotic environment in a series of reactions termed biogeochemical cycles (Clapham 1973, Brewer 1988) of which the carbon, nitrogen and phosphorus cycles are most pertinent from the perspective of this review. As most subterranean food webs are heterotrophic, transfer of carbon from particulate and dissolved organic matter to invertebrates is mediated by biofilms coating sediment particles and rock surfaces (Bärlocher and Murdoch 1989, Chafiq and Gibert 1996, Claret et al. 1998, Findlay and Sinsabaugh 1999). Biofilms transduce nutrients and energy (Battin et al. 2003) through processes including abiotic adsorption of molecules to the biofilm matrix and biological uptake by enzymatic hydrolysis. The bacterial uptake and repackaging of carbon and nutrients constitutes a microbial loop (Sherr and Sherr 1988) through which dissolved and particulate organic matter is made available to grazing protozoans and invertebrates. Carbon and nitrogen cycles are linked because most nitrogen in aquatic systems is bound in organic matter and is unavailable until it is mineralised to ammonium (NH4+) by the breakdown of organic matter (Duff and Triska 2000). Microbially-mediated geochemical cycles involve the transfer of electrons between compounds. The rate and direction of geochemical cycling depends on the availability of electron donors and acceptors. Under aerobic conditions, oxygen acts as an electron acceptor, but under anaerobic conditions other compounds are used as donors in a reduction sequence of nitrate, manganese, iron, sulphate and carbon dioxide (Wetzel 2001). Different reactions occur in oxic and anoxic conditions, and the co-occurrence over small spatial scales of coupled processes contributes to the characteristic patchiness of SGDEs. Microbially-mediated nitrogen cycling (Box 8) can occur as coupled nitrification-denitrification reactions along gradients of oxygenation (Baldwin and Mitchell 2000). Phosphorus dynamics are closely related to the cycling of iron, and therefore require anaerobiosis (Baldwin and Mitchell 2000). Rates of biogeochemical transformations are affected by factors such as temperature, pH or the presence of heavy metals. Box 8: Nitrogen processes in groundwater Nitrification is the bacterial oxidation of ammonium (NH4+). Ammonium is produced by excretion or the decomposition of organic matter. Denitrification is the bacterial reduction of nitrites and nitrates (NOx) either back to ammonium, or to nitrogen gas, which is then lost from the system. (Wetzel 2001) The spatial availability of electron donors is determined by patterns of water flow, which in turn, are driven by hydrologic connectivity and hydraulic conductivity (Baker et al. 2000a), key factors in our proposed typology. Water is a transport agent (Bakalowicz 1994) that percolates through the vadose zone, or pulses through the hyporheic zone, to deliver dissolved and particulate organic matter and dissolved oxygen to biofilms. Microbial activity is typically highest near the source of recharge and declines along a gradient with distance from it (Kaplan and Newbold 2000). In aquifers connected to surface waters, the hyporheic zone is a crucial interface for fluxes of nutrients (Boulton et al. 1998, Dahm et al. 1998, Fischer et al. 2005). Flood pulse inundation in a semiarid catchment in New Mexico altered rates of nutrient retention and organic matter processing in floodplain groundwater (Baker et al. 2000b). Local lateral exchange processes such as cycles of bank discharge and recharge can also play an important role in the timing and direction of nutrient processing in floodplains (Lamontagne et al. 2005b).



In unconfined alluvial aquifers with fluctuating watertables, a significant portion of organic carbon metabolism can occur in oxic–anoxic cycles in the zone of intermittent saturation (Vinson et al. 2007). Hydraulic conductivity also determines the availability of electron donors for biogeochemical processes. Interstitial storage of dissolved organic matter and the availability of dissolved oxygen are influenced by particle size and pore size (Maridet et al. 1996). Larger particle size and high porosity allow higher flows and higher availability of oxygen but reduce entrapment and retention of nutrients. In fractured rock and karstic aquifers, uneven porosity due to the distribution of fissures, fractures and solutional conduits creates preferential flow paths, which create spatial heterogeneity in biogeochemical cycling (Ayraud et al. 2006). Spatial and temporal variability in groundwater flow paths is also influenced by surface microtopography (Pfeiffer et al. 2006) and by stream channel morphology (Dahm et al. 1998). The functional diversity of subsurface ecological processes is thus determined by shifting gradients in oxygen, nutrients and physico-chemical conditions, which create pockets of oxia and anoxia, nitrification and denitrification. As in other ecosystems, heterogeneity in subsurface environments is a critical determinant of ecosystem function (McCarty et al. 2007). Disturbance to the groundwater regime, including disruption of patterns of hydrological connectivity (Baker et al. 2000b) and sediment wettingdrying cycles (Baldwin and Mitchell 2000), might potentially alter spatial and temporal patterns of groundwater flow, flux and quality, with implications for rates of organic matter mineralisation and nutrient cycling. Pumping from a fractured rock aquifer in north-west France caused physical disturbance to water flux in the aquifer, reduced groundwater residence time and subsequent drastic modification to the water chemistry resulting in less active biogeochemical processes (Ayraud et al. 2006). Prolonged desiccation of sediments caused by watertable drawdown is likely to alter the balance between aerobic and anaerobic processes and change the composition of microbial populations, reducing the incidence or rate of anaerobic metabolism. Fischer et al. (2005) concluded that carbon and nitrogen cycling in hyporheic sediments were central to the metabolism of a large lowland river in Germany, and designated the hyporheic zone as the ‘river’s liver’. Disturbance to the groundwater regime can alter the rate and nature of subsurface ecological processes, resulting in reduced availability of carbon, nitrogen and phosphorus, with flow-on effects for biodiversity and ecosystem services, not only within the aquifer, but also in connected ecosystems including rivers, riparian zones and estuaries.



4 Provision of goods and services

Ecosystem goods and services are the conditions and processes through which natural ecosystems, and the species that are part of them, help sustain and fulfill human life (Daily et al. 1997). Goods are tangible, direct benefits. Services are ecological functions that benefit humans. While goods can often 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, the goods and services provided by groundwater will gain value; but 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. This risk is exacerbated by the high probability of accelerating change in deterioration of ecosystem services. Further, irreparable damage might occur to ecosystem service providers (ESPs) if excessive water is removed or other impacts, not readily detectable, take place. The use of groundwater could continue in excess of recharge for some time before the escalating impacts of extraction become apparent. The main categories of ecosystem services (Millennium Ecosystem Assessment 2005) provided by groundwater (Table 3) are as follows: Table 3: Ecosystem services provided by groundwater
Type of service Provisioning Supporting Examples Water for drinking, irrigation, stock and industrial uses Bioremediation, ecosystem engineering, nutrient cycling, sustaining linked ecosystems, providing refugia Flood control and erosion prevention Religious and scientific values, tourism

Regulating Cultural

4.1 Provisioning services
Goods provided by subsurface ecosystems include drinking water, water for irrigation and stock watering, and water for industrial uses (National Research Council 1997). Total consumptive water use in Australia was 24,058 gigalitres in 1996–97 (Ball et al. 2001), 21,703 gigalitres in 2000–01 and 18,767 gigalitres in 2004–05 (National Water Commission 2006). About 20 per cent of total consumptive water use is from groundwater, with 10 per cent of this sourced from the Great Artesian Basin (Commonwealth of Australia 2007b). The quantity of groundwater extracted for stock and domestic use in Australia is largely unlicensed and unmetered. Adoption under the NWI of consistent metering and measuring of all water access entitlements, and the development of national metering specifications and standards, will improve the accuracy of water extraction data and provide better understanding of the extent of consumption of groundwater goods.

4.2 Supporting services
Bioremediation is 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, Andreoni and Gianfreda 2007). Common contaminants in aquifers are anthropogenic chemicals such as chlorinated solvents, polycyclic aromatic hydrocarbons (PAHs: naphthalene, phenanthrene, anthracene) resulting from the incomplete combustion of coal, oil, petrol, and wood (Bamforth and Singleton 2005), and volatile aromatics collectively designated as BTEX (benzene, toluene, ethylbenzene and xylene)



derived from chemical industries, industrial wastes and hydrocarbon storage and spillage (Andreoni and Gianfreda 2007). Bacterial bioremediation has been the subject of detailed studies (Meckenstock et al. 1999). Bioremediation of contaminants by aquifer bacteria occurs both aerobically and anaerobically (Andreoni and Gianfreda 2007), often at the edge of contaminant plumes (Griebler et al. 2007), where electron donors from the plume mix with electron acceptors from the surrounding groundwater across a steep physico-chemical gradient (Griebler et al. 2007). 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 can facilitate clogging (Mauclaire et al. 2006). The rate of movement of a contaminant also varies according to its solubility. PAHs have low water solubility, resist biodegradation and are highly persistent; BTEX are highly soluble and volatile and are more readily biodegradable (Bamforth and Singleton 2005, Andreoni and Gianfreda 2007). The role of other aquifer biota in bioremediation is not well understood, although protozoan grazing promotes biodegradation by stimulating bacterial activity (Mattison et al. 2005), and a similar role seems likely for stygofauna. European researchers are investigating the contribution of stygofauna to bioremediation in a mesoscale experiment (Schmidt et al. 2007a), in which groundwater will be run through heterogeneous aquifer material with its natural faunal community. A contaminant plume will be established, and the microbial and invertebrate contributions to biodegradation studied under conditions of varying permeability and therefore flow rate. Stygofaunal crustaceans were implicated 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). High numbers of crustaceans, particularly large-bodied isopods, occurred along a gradient downstream of the disposal site. The dominant species, an isopod, was found to ingest and digest live bacteria.

Biogeochemical processes
Processing of organic matter in alluvial aquifers and delivery of nutrients to streams through groundwater discharge contributes to surface GDEs by maintaining water quality for riparian, floodplain and instream vegetation (Baker et al. 2000b) and providing nutrients and dissolved organic matter to macrophytes (Hayashi and Rosenberry 2002). Many groundwater heterotrophic bacteria are able to reduce nitrate and also play an important role in the mineralisation of organic matter and other biogeochemical processes (Baldwin and Mitchell 2000, Mermillod-Blondin et al. 2005b). Ecosystem services of alluvial aquifers include the attenuation of high nitrogen inputs from anthropogenic sources, reducing nitrogen loading in the river. Denitrification (the reduction of nitrates) in groundwaters is important in regulating the export of nutrients into surface waters (Lamontagne et al. 2005b). Microbial involvement in the biogeochemical cycling of carbon has also contributed to the production of fossil fuels. Several methanogenic microbial communities have been identified in the deep subsurface, each adapted to particular salinity conditions and with preferential substrate use, and each inducing distinct geochemical groundwater signatures (Waldron et al. 2007).

Support to groundwater dependent ecosystems
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), aquatic communities in caves (Eberhard 2004), springs and springbrooks (Meyer et al. 2003), terrestrial vegetation (Wischusen et al. 2004, Lamontagne et al. 2005a, O'Grady et al. 2006b), and it supports estuarine and marine ecosystems. Groundwater is a significant component of summer flow in the Swan-Canning Estuary in Western Australia (Linderfelt and Turner 2001). Thermal and salinity anomalies due to seeping intertidal groundwater in coastal Delaware, USA, create habitat differences equivalent to a northward latitudinal shift of 250 kilometres in summer and a southward 380-kilometre shift in winter,



with implications for biological productivity, faunal distribution and community composition of benthic biota (Dale and Miller 2007).

Ecosystem engineering
Grazing of biofilm by stygofauna is postulated to prevent overgrowth of biofilm and consequent sediment clogging, as demonstrated for a soil flagellate by Mattison (2002). Stygofaunal grazing may also stimulate biofilm activity, thus maintaining biofilm function (Edler and Dodds 1996). Bacterial activity also affects the physical and hydraulic properties of aquifers through the production or dissolution of intergranular cements (Chapelle 2000). Benthic and hyporheic fauna alter the physical and hydraulic attributes of their habitat through mechanical bioturbation and pelletisation (Mermillod-Blondin et al. 2003, Mermillod-Blondin et al. 2004a, Mermillod-Blondin et al. 2004c, Nogaro et al. 2006), helping to maintain flow by preventing sediment clogging (Mattison et al. 2002, Hancock et al. 2005, Mauclaire et al. 2006), and thereby contributing to the sustainability of water supply for a range of consumptive and non-consumptive uses (Caliman et al. 2007). A similar role for stygofauna has been suggested (Boulton et al. 2008) but not yet tested experimentally.

Some surface aquatic taxa resist water loss and desiccation by migration into moist or saturated refugia including SGDEs. Boulton et al. (1992) suggested that the dry channel hyporheic biotope provides a crucial refuge from drought for some surface-dwelling invertebrates in temporary streams with sandy or gravel substrates. For example, surface water amphipods (Harris et al. 2002) and hyporheic invertebrates (Clinton et al. 1996) survive the drying of ponds by migrating into deeper sediments with the falling watertable. Crayfish burrows full of water provide refugia for some stream insects (Boulton and Lake in press) and for the syncarid Allanaspides hickmani, which lives in seasonally ephemeral pools in button grass moorland in Tasmania (Driessen and Mallick 2007). Fish in floodplains of the east Kimberley retreat to karst sinkholes during the dry season (Humphreys 1995). The eskers of Finland are identified by Sarkka and Makela (1999) as refugia and possible pathways for faunal dispersal between alpine and arctic areas. Groundwater discharge into estuaries can provide refuge zones for saline-sensitive species during periods of hypersaline conditions associated with reduced river discharge during droughts (Taylor et al. 2006). On an evolutionary scale, aquifers have provided refugia from changing environmental conditions on the surface, including the onset of aridity in Australia (Cooper et al. 2002, Cooper et al. 2007, Finston et al. 2007).

4.3 Regulating services
Flood control and erosion prevention
As receptors, storages, and transmitters of recharge, aquifers regulate parts of the hydrological cycle, absorbing runoff and mitigating the impact of storm events. Aquifer storage of runoff and streamflow is particularly significant in zones of strong groundwater–surface water connections such as riverbanks and floodplains (Brunke and Gonser 1997, Sophocleous 2002). During flooding, rivers lose water to the riverbanks or, if the banks are over-topped, to the floodplain. During dry periods, these aquifer storages release water back to the river, helping to compensate for reduced river flow. This ‘buffering effect’ reduces the rate of change (or ‘flashinesss’) of stream discharge, with important hydrological repercussions for surface fauna and processes (Bunn and Arthington 2002).



4.4 Cultural services
Ecological indicators
Stygofauna have the potential to offer a service as indicators of ecosystem condition and the integrity of some of the fundamental ecological processes occurring in groundwaters. The use of aquatic macroinvertebrates as indicators of river health is well-established (see discussion of the river health concept in Boulton (2000b)), but currently, river health assessment does not include an examination of the ‘health’ or condition of hyporheic zones (Boulton 2000b, Hancock 2002) or aquifers. Application of the river continuum concept suggests that inclusion of these components would enhance the robustness of river health assessment (Reid and Brooks 2000), especially in ephemeral arid zone rivers with subsurface flow. For aquifers, Gibert et al (1994) indicate that the relative stability of systems and high degree of specialisation of fauna suggests that stygofauna will be sensitive to environmental change. The relative abundance of surface water and groundwater forms can be related to the flow patterns of pollutants (Malard et al. 1994, Malard et al. 1996). Dumas et al. (2001), investigating the impacts of agricultural pollutants in the Ariège alluvial aquifer in the French Pyrénées found that macrocrustaceans constitute natural indicators of aquifer hydrodynamics; a dominance of stygobites indicates low surface water inputs, and so could indicate the absence of nitrate-enriched surface water in aquifers (Claret et al. 1999a). Organic pollution from surface waters allows invasion by surface water forms, forcing stygobites into oligotrophic refugia. Surface water cladocerans (water fleas) predominate in the hyporheos of polluted reaches of the Rhône (Schmidt 1994). No syncarids were found in groundwater below a sewage bed in New Zealand (Scarsbrook and Fenwick 2003), indicating that syncarids might be sensitive to high levels of nutrients. These responses could well be taxa-specific as Dumas and Lescher-Moutoue (2001) found little apparent effect of nitrates on cyclopoids in the Ariège aquifer, with acute toxicity occurring only at levels greater than 200 milligrams per litre. (For comparison, the maximum limit for nitrates in drinking water is 45 milligrams per litre in the USA (Manassaram et al. 2006) and 50 milligrams per litre in Australia (National Health and Medical Research Council 2004)). If stygofauna are more sensitive than surface water fauna to chemical pollutants (Mosslacher 2000), groundwater quality criteria based on responses of surface water organisms could be insufficient to be used to protect groundwater systems (Hose 2005). The use of stygofauna as biomonitors of heavy metal contamination has been explored in several studies in Europe (Plénet and Gibert 1994, Plénet et al. 1996, Canivet et al. 2001, Canivet and Gibert 2002), but there is no equivalent work in Australia. Plénet (1999), working under laboratory conditions with fauna collected from the Rhône River catchment, found that a stygobitic amphipod was less sensitive than a surface water amphipod to zinc and copper concentrations, perhaps this was due to differences in metabolic rates. Nevertheless, the lower metabolic rates of stygobites could mean that longer exposure might be required before toxic effects are evident (Hose 2007).

Indigenous cultural values
Groundwater has strong cultural values in Indigenous Australia. 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 Australian arid zone, where stream flow is ephemeral, groundwater in streambeds supplied drinking water, and diffuse discharge supports important food species such as the EPBC-listed Ipomoea sp. Stirling (Department of the Environment, Water, Heritage and the Arts 2008). The Indigenous relationship with aquatic systems can be understood as a socio-ecological relationship that is equivalent to kinship relations of obligation and care (Jackson 2006), suggesting that contemporary Indigenous communities are likely to have cultural reasons for involvement in groundwater management.



Tourism and recreation
Cave tours began in Australia in the 19th century and continue as a major tourism activity today (Finlayson and Hamilton-Smith 2003). Jenolan Caves is the most visited cave system in Australia, with more than 250,000 visitors annually. This is a significant proportion of the 750,000 paid visits to caves every year (Spate 1989). An unknown number of ‘wild’ cave visits is made by individuals and members of caving organisations; the Australian Speleological Federation Inc. has about 1000 members and 32 constituent bodies (Finlayson and HamiltonSmith 2003). Western Australia’s largest tourism cave, Jewel Cave (Box 9), presents an interesting case study of the challenges of managing SGDEs. Box 9: Case study 1 – Jewel Cave Western Australia Location: 34° 17’ S, 115° 07’ E The Jewel Cave karst system in southwest Western Australia houses a stygofaunal community associated with submerged eucalypt tree roots. This aquatic root mat community is one of four listed as threatened under the Commonwealth Environment Protection and Biodiversity Conservation Act 1999 because of declining groundwater levels. A multi­ disciplinary investigation of this SGDE found that groundwater abstraction was not contributing to the water decline as had been previously suggested. Besides a major decrease in rainfall over several decades, the declining water levels were possibly also influenced by a changed fire regime within the catchment. Fire management practices changed from regular hazard reduction burns undertaken every year or so over many decades, to no hazard reduction burns. The absence of fire allowed dense growth of understorey vegetation and an accumulation of ground litter that contributed to reduced groundwater recharge through interception of rainfall and increased evapotranspiration. The study concluded that conservation actions for this threatened SGDE need to be focused at the most appropriate spatial scale, which is the karst drainage system and catchment area. Since this study, rainfall in southwest Western Australia has continued to decline markedly, and long-term climate modelling suggests this trend will continue, possibly exacerbated by anthropogenic climate change. The groundwater levels in the Jewel Cave are presently at a critically low level, with virtually all known habitat and occurrences of the aquatic root mat community having dried up or likely to disappear in the near future. (Eberhard 2004, Eberhard 2005)



5 Management of SGDEs
5.1 Conservation
In Australia there are obligations to conserve subterranean fauna and communities if the provisions of the Commonwealth Environment Protection and Biodiversity Conservation Act 1999 (EPBC Act) are triggered (Box 10). Under this Act, environmental assessment is triggered by an action that is likely to have a significant impact on matters of national environmental significance protected under Part 3 of the Act. These matters include threatened species and ecological communities listed in accordance with Schedule 1 of the Act. Lists maintained under territory and state law have no bearing in this context. There are numerous obstacles to effective conservation of stygofaunal biodiversity, including: shortage of taxonomists, lack of knowledge of reference conditions, lack of knowledge about microbial assemblages, lack of data from replicated surveys, incomplete coverage of habitat types, lack of standardised protocols for sample collection and processing, lack of identification keys, a need for centralised repository of reference material, and a need for a central database adhering to nationally-agreed standards (Tomlinson et al 2007a). Further, groundwater management in Australia to date has seldom involved ecologists, so data collection and assessments have not been done with an ecological perspective that recognises small-scale differences within habitats, or differences between habitat types. These challenges limit the application of stygofaunal research in management, yet it is only by continued strategic research, including targeted surveys (Tomlinson et al. 2007a), that management applications will be developed. Box 10: EPBC Act listing of stygofaunal species and groundwater-dependent ecological communities Species listed under the EPBC Act are: • Three stygofaunal species from Western Australia: – – – • the remiped crustacean Lasionectes exleyi the Blind Cave Eel Ophisternon candidum the Blind Gudgeon Milyeringa veritas.

Five subsurface groundwater dependent communities in Western Australia (four root mat communities in caves of the Leeuwin-Naturaliste Ridge and one root mat community in caves on the Swan Coastal Plain). At least four communities with some dependence on groundwater: – – – – temperate highland peat swamps on sandstone the thrombolite (microbial) community of coastal freshwater lakes of the Swan Coastal Plain (Lake Richmond) the community of native species dependent on natural discharge of groundwater from the Great Artesian Basin assemblages of plants and invertebrate animals of tumulus (organic mound) springs of the Swan Coastal Plain.




5.2 Threatening processes and SGDEs
A threatening process (Box 11) is defined in the EPBC Act as a process that threatens or could threaten the survival, abundance or evolutionary development of a native species or ecological community. The intimate hydrological and functional connections between SGDEs and other ecosystems indicate their reciprocal vulnerability to threatening processes at the surface and in the groundwater. Box 11: Threatening processes in SGDEs Disturbance to the groundwater regime can result in: • • • • • • increases in salinity pollutants (for example, heavy metals) in discharging groundwater increased nitrates causing eutrophication in receiving waters reduced connectivity to dependent ecosystems land subsidence loss of groundwater habitat.

Changes in the quantity and quality of recharge impact on the key groundwater attributes of flux or flow, level (in unconfined aquifers) or pressure (in confined aquifers), and quality. Impairment of groundwater flow, quantity or quality can potentially affect the resilience of connected systems, not only by direct effects such as input of contaminants but also indirectly by altering the pathways for resource capture and energy flow (Brookes et al. 2005). The magnitude of impacts could be exacerbated by the inertia of many groundwater bodies. Slow groundwater flow rates and the thickness of the saturated zone result in time lags before the impacts of pressures such as extraction are apparent, and parallel time lags before management improvements take effect. For example, nitrate concentrations in an Iowa watershed in the 1990s were still influenced by heavy application of nitrogen fertiliser 30 years previously (Tomer and Burkart 2003). Without careful monitoring, tolerance thresholds could be crossed and goods and services lost before the impacts of intensifying threats are evident. The mechanism and extent of dryland salinity in Australia is well-known (for example, see Clarke et al. 2002in relation to Western Australia). Groundwater recharge has increased due to widespread land clearing, the replacement of deep-rooted native vegetation with shallowrooted pasture or crops, and responses to irrigation and river regulation (Jolly et al. 1993). Rising water levels intercept salt stored in the former unsaturated zone, or bring naturally saline water to the surface, resulting in salinisation of soils and streams. Deep, marinesourced aquifers can also be sources of salinity where seepages originate from fractured bedrock (Morgan et al. 2006). Input of saline groundwater is a substantial threat to the biodiversity of surface wetlands and rivers (Halse et al. 2003), and can drive shifts in faunal assemblage towards more salt-tolerant taxa, with an associated shift in feeding group composition which has implications for trophic linkages in the receiving waters (Boulton et al. 2007). Salinisation may also occur due to seawater intrusion into coastal aquifers under pressure from extraction. For example, considerable seawater intrusion has already occurred in coastal aquifers near Bundaberg, Queensland, where groundwater has been extracted since 1958 for irrigation, industrial use and urban water supply. Salinisation was first detected during a dry period in the 1960s. During succeeding years of below-average rainfall, groundwater levels were drawn below sea level by more than three metres for a period of more than 15 months, inducing further seawater intrusion (Zhang et al. 2004). Discharging groundwater can be a source of metals derived from leachate from landfill, pollution by earlier mining and ore processing (Coynel et al. 2007), or from solution of metals in fresh fractures caused by mining-induced subsidence (Jankowski and Spies 2007). Elevated concentrations of nitrates leached from agricultural fertilisers and from urban and



industrial point sources occur widely in groundwater in many parts of the world, including Australia (Burkart and Stoner 2002, Scanlon et al. 2007). Increased nitrate levels in drinking water threaten human health (Manassaram et al. 2006), and together with increases in phosphate levels in discharging groundwater, likely contribute to eutrophication in freshwater, estuarine and marine discharge zones (Valiela et al. 1990, Linderfelt and Turner 2001, Slomp and Van Cappellen 2004, Rasiah et al. 2005). Eutrophication causes a loss in the ecosystem goods and services, including recreational and potable uses of the receiving waters (Rast and Thornton 1996). Human disturbance to the hydrological cycle often results in a cascade of effects in aquatic and terrestrial systems. These include habitat loss, degradation or fragmentation, altered water quality and reduction or cessation of baseflow and spring discharge (Pringle 2001). Reduced groundwater discharge threatens the ecology and biodiversity of many wetlands and rivers by limiting connectivity, affecting stream metabolism and failing to support dry season refugia (Boulton and Hancock 2006). By 2000, groundwater exploitation had caused cessation of flow in one third of the 3000 natural springs of the Great Artesian Basin (Wilmer and Wilcox 2007), resulting in the listing of mound springs communities under Commonwealth endangered species legislation. Increasing demand for groundwater extraction resulting in decreased storage volumes or deterioration in quality also potentially impacts groundwater-dependent terrestrial vegetation and associated fauna. Groom et al. (2000) investigated the effect of lowered water levels due to extraction combined with poor recharge following low rainfall on the Banksia woodland overlying the Gnangara Mound, a shallow, unconfined aquifer near Perth. Extensive death of overstorey and understorey species coincided with a lowering of groundwater level by 2.2 metres, with no significant decreases in the abundance of overstorey or understorey species recorded in a monitored site not influenced by groundwater extraction. Monitoring data from a 20 to 30 year period indicated that changes in species distribution and vigour were primarily caused by long-term declines in groundwater levels resulting from the cumulative effects of extraction and below average annual rainfall (Groom et al. 2001). Impaired surface vegetation biomass and land cover can trigger a cascade of impacts, including reduced subsurface supply of organic matter and changes in runoff and recharge. Groundwater extraction can result in land subsidence due to loss of pressure in the aquifer and surface soil compaction. Large-scale pumping of groundwater from aquifers in the Port Adelaide region during the last 50 years is associated with ground subsidence of 2.5 millimetres per year, with a maximum subsidence of 10 millimetres per year where groundwater withdrawal coincides with wetland reclamation (Belperio 1993). Loss of storage volume and lowering of water levels through overextraction necessarily reduces habitat for stygofauna.

5.3 The potential impact of climate change
The projected changes in Australia’s climate due to global warming that are summarised in this report are based on simulations by nine different climate models (Commonwealth of Australia 2003). Changes in annual average rainfall by 2030 are predicted to be in the range of –20 to +5 per cent in southwest Australia and –10 to +5 per cent in south-eastern Australia. By 2070, changes in the range of –60 to +10 per cent are predicted in south-western Australia and –35 to +10 per cent in south east Australia. Annual average temperature is predicted to increase by 0.4 to 2° C by 2030 and by 1 to 6° C by 2070. Projections for northern and inland Australia are indefinite, but the impacts of climate change are likely to vary from locality to locality. Increased evaporative stress is expected with increased temperatures. There is also a predicted increase in frequency in extreme weather events with associated increased incidence and severity of flooding and erosion. Climate models suggest that drought could be as much as 20 per cent more common by 2030 over much of Australia and up to 80 per cent more common in south-western Australia by 2070. Finally, a sea level rise of between nine and 88 centimetres is predicted by 2100. The vulnerability of SGDEs to climate change can be expected to vary with habitat type. Highly transmissive, unconfined aquifers near the coast will be more sensitive to changes in recharge, surface water temperatures and sea level rise than deep inland aquifers with low



rates of recharge and throughflow. Although the ability to predict the effect of climate change on groundwater is limited by uncertainties between models (Crosbie 2007), the most direct impact will be on recharge, with a change in recharge in the same direction as a change in precipitation. Potential changes in recharge versus rainfall are highly nonlinear and vary with soil type and vegetation (Green et al. 2007). In general, decreasing rainfall and increasing temperatures suggest a decrease in runoff and recharge. Projected reductions in runoff vary from seven to 35 per cent in Melbourne, 10 to 25 per cent in the Murray-Darling Basin and 31 per cent in the Stirling catchment (Western Australia) (Commonwealth of Australia 2007a). Since the late 1960s, mean annual rainfall in southwest Western Australia has declined dramatically, and river flows have reduced by almost three times the reduction in mean rainfall. That is, an average rainfall decline of 10 to 20 per cent caused a 40 to 60 per cent decline in dam inflow (Commonwealth of Australia 2007a). Groundwater storage volumes can be expected to decrease due to loss of recharge, with a parallel decrease in capillary rise to vegetation and a loss of discharge to springs and streams. Lowered groundwater input to streams could alter hydraulic gradients between the stream and connected aquifers. Sustained reduction in recharge and increased evapotranspiration will result in groundwater drought, with complex and diverse consequences (Peters et al. 2003). Drought attenuates the flushing of nitrates and dissolved organic carbon into groundwater, limiting microbial metabolism and reducing the supply of energy and nutrients to streams (Dahm et al. 2003). Greater frequency of drought will exacerbate demand on groundwater resources and intensify competition between consumptive and non-consumptive uses of groundwater. Reduced streamflow and higher surface water temperatures will potentially be associated with increased eutrophication of surface waters, with implications for changed rates of benthic processes. Effects of surface warming can be expected to be particularly strong in summer in groundwater-fed streams, with increases in mean annual oxygen consumption, rates of mineralisation and higher bacterial biomass (Sand-Jensen et al. 2007). Surface warming in groundwater recharge areas could elevate subsurface temperatures, with likely impacts on rates and dominance by different biogeochemical processes and on subterranean microbes and fauna adapted to narrow zones of thermal stability. Higher surface water temperatures will result in reduced levels of dissolved oxygen, with probable impairment of suitable conditions for the hyporheos in downwelling zones. Higher groundwater temperatures will be associated with a decrease in viscosity and a resulting increase in hydraulic conductivity (Freeze and Cherry 1979), with implications for enhanced transport of solutes and contaminants. In areas where rainfall and the severity of storms is expected to increase, higher rates of recharge will result in increases in flux in aquifers and potentially elevated rates of nitrate leaching; erosion will increase leading to higher sediment loads in streams, perhaps hampering groundwater–surface water exchange; and increases in storage may exacerbate dryland salinity. It is also possible that increased rainfall in arid and semi-arid regions will stimulate biomass productivity, resulting in no nett increase to groundwater recharge (Scanlon et al. 2006). Sea level rise will result in increased salinisation of surface and ground waters in coastal and island regions, a rise in coastal groundwater levels and inland movement of the underlying saline lens resulting in reduced water quality, possibly threatening GDEs associated with coastal aquifers. Salt-water intrusion will be exacerbated by lowered level or pressure due to groundwater drought, particularly in aquifers under pressure of extraction. Both Crosbie (2007) for Australia and Puri (2006) speaking globally suggest that the direct impact of climate change on groundwater will be less significant than the impacts of associated pressures such as increasing consumptive demand, land clearing, urbanisation and other factors impacting on hydrological cycles. McMahon and Finlayson (2003) consider that even if the most extreme predicted climate change scenarios for Australia were to eventuate, their impact and rate of onset, at least for surface waters, would be on a lesser scale than the changes that have already occurred as a result of river regulation.



5.4 Current policy setting in Australia
Australian states and territories are constitutionally responsible for natural resource management. The Commonwealth drives the co-ordination of natural resource management by linking National Competition Council payments with jurisdictional progress towards institutional reforms agreed by the Council of Australian Governments (COAG), and through strategic investment under the $2 billion Australian Government Water Fund administered by the NWC and the Commonwealth Department of the Environment, Water, Heritage and the Arts. The water reforms agreed in 1994 require that water must be allocated for environmental use first, having regard for nationally-agreed principles (ARMCANZ/ANZECC 1996) and based on best available science. By April 2006, all Australian jurisdictions had signed the Intergovernmental Agreement on a National Water Initiative (NWI), under which the COAG reforms are to be carried forward. The NWI commits participating jurisdictions to a number of actions, including the development of water plans that include a specific provision for water to meet environmental and other public benefit outcomes, and a definition of the appropriate water management arrangements to achieve those outcomes. Implementation of the NWI is now underway across Australia. All jurisdictions have now made legal provision for environmental water (Table 4) and are developing water plans to meet environmental outcomes. The NWI states (in Schedule B(ii)) that environmental outcomes can include: maintaining ecosystem function (for example, through periodic inundation of floodplain wetlands) and targets for biodiversity, water quality; and river health. These are congruent with the main subject areas of this review: biodiversity, subsurface ecological processes, and ecosystem goods and services. Table 4: Legislation and policy addressing NWI requirements regarding environmental water
Jurisdiction Legislation relating to water planning Water Management Act 2000 Policy documents relating to environmental provision State Water Management Outcomes Plan 2002NSW State GDE Policy Qld Water Plan 2005–2010 Water for Ecosystems Policy 2001 State Water Plan 2007 Statewide Policy No. 5 State Natural Resources Management Plan 2006 Our Water, Our Future No specific policy document; policy approach outlined in individual water resource plans Water Resources Management Plan 2004 Environmental Flow Guidelines 2006

New South Wales

Queensland Tasmania

Water Act 2000 Water Management Act 1999

Western Australia

Rights in Water and Irrigation Act 1914 Natural Resources Management Act 2004 Water Act 1989 Water Act 1992

South Australia

Victoria Northern Territory

Australian Capital Territory

Water Resources Act 2007

States and territories have prepared NWI implementation plans (National Water Commission 2007b) in accordance with guidelines provided by the NWC. The basic framework for integrated and sustainable groundwater management is being established through extraction



licensing, bore metering, and arrangements for data storage. Actions taken to implement NWI objectives relating to environmental management of groundwater address legislative changes and other administrative matters that establish the foundation for groundwater management, but there are few indications of actions to identify GDEs, let alone to assess their environmental water requirements. This is unsurprising given the paucity of basic data on groundwater extraction, the historical separation of surface water and groundwater management (a symptom of ‘hydroschizophrenia’ (Box 12)), the knowledge gaps relating to GDEs and the scant scientific guidance on assessment of environmental water requirements. Box 12: Symptoms of hydroschizophrenia • • • separate management of surface and groundwater playing down the role of groundwater poor and uncoordinated transboundary groundwater management.

(Jarvis et al. 2005, Llamas and Martinez-Santos 2005) The inability to specify rules for managing environmental groundwater flows or to specify suitable indicators for monitoring responses to aquifer management had already been identified (National Groundwater Committee 2004). Australian research effort concerned with GDEs has focused on assessing groundwater dependency of terrestrial GDEs (Zencich et al. 2002, Lamontagne et al. 2005a, Cook and O'Grady 2006, O'Grady et al. 2006b). The only guidance documents in Australia regarding SGDEs are the NSW GDE policy (Department of Land and Water Conservation 2002) and a Western Australian document and technical appendix providing guidance for consideration of subterranean fauna during environmental impact assessments (Environmental Protection Authority 2003, 2007). The NSW policy sets out principles and a general framework for GDE management but lacks a detailed work plan, which would deliver tools and guidelines for effective implementation. The Western Australian guidance document addresses the specific situation of environmental impact assessment, and although useful in describing sampling methods and survey design, is not directly applicable to the needs of statutory water planning. The first biennial assessment of progress in implementation of the NWI (National Water Commission 2007a) found that arrangements for the management of environmental water had not yet emerged as envisaged by the NWC, that environmental water sustainability deserved renewed attention, and that a more harmonised and rigorous national approach to monitoring river health and groundwater is required. It was recommended that action be taken to ‘improve understanding of groundwater and management of groundwater-surface water interaction’ and to ‘improve and harmonise river health and groundwater ecosystem monitoring and assessment to enable states to incorporate information from this monitoring into their adaptive management frameworks’. A key process in defining the water needs of GDEs is the identification of environmental water requirements (EWRs), analogous to the concept of environmental flows for surface water. The EWR is the water regime needed to maintain ecological values and ecosystem services of water dependent ecosystems at a low level of risk (SKM 2001). EWRs are determined on the basis of the best scientific information available and are the primary consideration in the determination of environmental water provisions (EWPs), which are the water regimes provided as a result of the water allocation decision-making process taking into account ecological, social and economic impacts. The EWPs can meet the EWRs in part or in full. Development of approaches to providing environmental flows or EWRs in aquifers associated with GDEs is at an early stage in Australia, and no research to date has focused on the water requirements of stygofauna (although see Box 17). The starting points in estimation of EWRs for GDEs are assessing the key attributes of flux, level or pressure, and water quality, and explicitly describing their roles in relation to the processes that drive the structure and function of dependent ecosystems. In the conceptual framework of SKM (2001), thresholds are determined for responses to change in water regime. The EWR is the water regime that maintains responses within ‘limits of acceptable change’. For SGDEs, there is a lack of baseline environmental and faunal data as well as knowledge gaps on community resilience to environmental change such as altered recharge, the impacts of groundwater extraction, tolerances to ranges of driving variables (dissolved



oxygen, nutrients, electrical conductivity, salinity, water level fluctuations), and tolerance to contaminants (see Figure 1). In the absence of these data, the limits to acceptable change must be set conservatively and perhaps by proxy through the EWRs for connected terrestrial water-dependent habitats. The multiplicity of connections between SGDEs and other systems described above (see the section on threatening processes) argues for consideration of SGDEs, if only to prevent harm to other systems. Table 5 lists the four (out of ten) NWI objectives concerned most directly with environmental management of groundwater (Box 14), the consequent NWI outcomes and NWI actions, and actions reported in the State and Territory Implementation Plans to address these. Objective iii) is in two parts: statutory provision for environmental and other public benefit outcomes, and improved environmental management practices. Action to address the first part involves reform of existing water legislation or the introduction of new legislation (Table 4). Box 14. NWI requirements most relevant to groundwater management • • • • make statutory provision for water plans and improve adaptive management address overallocation identify high conservation value systems recognise connectivity with surface water

Action to improve environmental management practices is less straightforward, being predicated not only on the identification of environmental outcomes, including maintenance of ecosystem function, biodiversity, and water quality, but also on an understanding of the water management practices that support these outcomes. However, some actions to identify GDEs and assess their water needs are reported by the jurisdictions. These projects will be supported by actions to return previously overallocated and/or overdrawn surface and groundwater systems to environmentally-sustainable levels of extraction (objective iv), arrangements for data collection and storage to improve water accounting (objective vii), and assessments of groundwater-surface water interconnection (objective x). Although the level of detail of GDE investigations is perhaps sufficient to meet broad reporting requirements, it is inadequate to assess their scale and scope at an ecologically relevant level. More detailed reporting at workshops and in publications including websites would provide a more reliable and useful picture of the status of GDE investigations, facilitate sharing of methods, techniques and experiences, and help indicate knowledge gaps and priority areas for research effort.



Table 5: NWI objectives and actions relevant to environmental management of groundwater, and actions reported in jurisdictional NWI implementation plans

Plans as accredited in 2005 (South Australia), 2007 (Western Australia), all other jurisdictions in 2006. Numbering of paragraphs is retained from the NWI and the respective Implementation Plans.

NWI objective iii) statutory provision for environmental and other public benefit outcomes and improved environmental management practices

NWI outcome 25 (ii) provide a statutory basis for environmental and other public benefit outcomes in surface and groundwater systems to protect water sources and their dependent ecosystems (iv) provide for adaptive management of surface and groundwater systems in order to meet productive, environmental and other public benefit outcomes 25(x) identify and acknowledge surface and groundwater systems of high conservation value, and manage these systems to protect and enhance those values

NWI action 35. Water that is provided by the states and territories to meet agreed environmental and other public benefit outcomes as defined within relevant water plans is to: i) be given statutory recognition and have at least the same degree of security as water access entitlements for consumptive use and be fully accounted for ii) be defined as the water management arrangements required to meet the outcomes sought, including water provided on a rules basis or held as a water access entitlement 37(i) Broadly, water planning by states and territories will provide for: i) secure ecological outcomes by describing the environmental and other public benefit outcomes for water systems and defining the appropriate water management arrangements to achieve those outcomes 79(i) (f) Identification of high conservation value systems (including rivers, reaches and groundwater areas)

Actions reported in NWI Implementation Plans ACT: Environmental and other public use benefits are described in the Territory Plan and Environmental Flow Guidelines. Actions to achieve the benefits are implemented through the ACT’s water plan. Water resource management in the ACT treats groundwater and surface water systems holistically ensuring that an overuse of one part of the resource cannot have a negative impact on the other. Maximum extraction limits have been determined conservatively and on the basis of the best scientific knowledge available in each review of the resource management plan NSW: Planned environmental water is provided for by rules in water sharing plans (for example, … reservation of a proportion of the sustainable yield in groundwater systems). For five inland groundwater systems, studies assessed the sustainable yield and identified groundwater dependent ecosystems. Pilot studies on the impact of planned environmental water on the health of groundwater dependent ecosystems are also being undertaken NT: Research work on identification of groundwater dependent ecosystems and Indigenous rights and values in water resources will continue as part of the work program for the declared water allocation plan for the Ti Tree Water Control District. The outputs of this research will be taken into account in the revision of the water allocation plan in 2007. Explicit recognition of high conservation-value rivers (and associated groundwater systems) will be at the core of the Government’s new Living Rivers Program, as well as a consideration in the review of the Water Act. Collaborate with SA to complete groundwater models for the Great Artesian Basin to determine environmental water requirements and predict impacts on mound springs from any planned development in the NT, by June 2009. SA: A ‘stressed resources’ methodology has been prepared for groundwater, surface water and watercourses but further work is required to refine the methodology for identifying stressed water-dependent ecosystems



NWI objective

NWI outcome

NWI action

Actions reported in NWI Implementation Plans Tas: Currently trialing an extraction licensing system; will develop a strategy in relation to the protection of groundwater dependent ecosystems through water management plans. Ongoing consideration of groundwater dependent ecosystems through Conservation of Freshwater Ecosystems Values Project Vic: Review groundwater activities and resources by late 2007.Ongoing licensing of extraction for commercial or irrigation use Qld: Water resource plans (WRPs) and Resource operations plans (ROPs) either have been or are currently being developed for virtually all heavily allocated systems, including areas with high levels of groundwater use. Groundwater resources are included in only one WRP (the Barron catchment) at this stage. In the Pioneer, Lockyer valley, Gulf, Mitchell and Bundaberg groundwater areas, groundwater management arrangements are being prepared for integration with water resource plans. The interconnected nature of groundwater and surface water is being considered and the water needs of the environment are being included to the extent that dependency exists. Ecological outcomes are stated in each WRP and supported by environmental flow strategies. The associated ROP requires that the achievement of the ecological outcomes be monitored, assessed and reported. The approach used to estimate the risk to the state’s groundwater resources involves ranking the groundwater systems according to their level of allocation compared with recharge, vulnerability to threats such as seawater intrusion, rising watertables, threats to groundwater dependent ecosystems and local issues such as local pumping effects, development pressures or community conflicts. WA: investigations and assessments including mapping of groundwater dependent ecosystems is underway. Water to meet environmental and other public benefit outcomes identified in water plans to be defined, provided and managed by 2009. Actions already taken: identification of groundwater dependent environmental features and ecological processes regarded as culturally and socially important to Indigenous communities as part of studies of the Gnangara Mound and South West Yarragadee aquifer, including how indigenous cultural values may be affected by changes in water level



NWI objective iv) complete the return of all currently overallocated or overused systems to environmentallysustainable levels of extraction

NWI outcome 25 v) implement firm pathways and open processes for returning previously overallocated and/or overdrawn surface and groundwater systems to environmentallysustainable levels of extraction

NWI action 95 States and territories agree that substantial progress will be made by 2010 towards adjusting all overallocated and/or overused systems in accordance with the timelines indicated in their implementation plans

Actions reported in NWI Implementation Plans Qld, ACT and NT: no known over-allocated systems NSW: Development of Water Sharing Plans by 2007 for systems that are overallocated, fully allocated or approaching full allocation and development. SA: Northern Adelaide Plains Prescribed Wells Area and the Padthaway Prescribed Wells Area are currently experiencing negative resource and environmental impacts which may be attributed to overallocation. The respective water allocation plans are being reviewed and will be amended with completion expected towards the end of 2006–07. Tas: in most parts of the state, groundwater use is well within sustainable limits. Currently an integrated licensing system is under development and will be implemented where groundwater resources are under stress or need to be managed in a fully coordinated way with surface water. It will be trialled in the Mella and Great Forester catchments. Vic: For rivers and aquifers currently not overallocated, Victoria will establish an environmental water reserve using a precautionary approach, establishing how much the environment needs and setting sustainable limits on extractions from that water system; and for stressed rivers and aquifers, Victoria will cap diversions at existing levels of entitlements and determine whether further water recovery to enhance the environmental water reserve is required in priority stressed rivers. WA: Statewide audit of groundwater licences by January 2009. Management areas containing overallocated resources have been prioritised for plan development, based on review of the allocation levels against allocation limits across the state. Areas previously considered as fully but not overallocated have been classified as overallocated due to improved understanding of climate change impacts or scientific knowledge of the resource.

vii) water accounting which is able to meet the information needs of different water systems in respect to planning,

80 The Parties agree that the outcome of water resource accounting is to ensure that adequate measurement, monitoring and reporting systems are in place in all jurisdictions, to support

82 iii) Water resource accounts that can be reconciled annually and aggregated to produce a national water balance, including: a) a water balance covering all significant water use, for all managed water resource systems

ACT: Accounting of groundwater and surface water use has been implemented and integrated. NSW: Accounting can be completed when the extent and connectivity of the interaction between surface and groundwater is determined and groundwater sources are subject to a water sharing plan. NT: Undertaking a range of studies to quantify groundwater and surface water connectivity. Once the connectivities are understood, the Northern Territory will



NWI objective monitoring, trading, environmental management and on-farm management

NWI outcome public and investor confidence in the amount of water being traded, extracted for consumptive use, and recovered and managed for environmental and other public benefit outcomes

NWI action b) systems to integrate the accounting of groundwater and surface water use where close interaction between groundwater aquifers and streamflow exist 85. The Parties further agree to develop by mid-2005 and apply by mid-2006: i) a compatible register of new and existing environmental water … showing all relevant details of source, location, volume, security, use, environmental outcomes sought and type

Actions reported in NWI Implementation Plans incorporate them into integrated water accounting for connected systems. SA: Ongoing projects and initiatives supporting water information management including enhancing the groundwater database, replacing loggers, and piloting web feature services. Tas: Development of groundwater registers as required for water management planning and for relevant groundwater areas, and development of a driller’s licensing system. Qld: Implement systems to integrate the accounting of surface and groundwater by the end of 2008. Vic: Meter all significant surface water and groundwater diversions. Implement systems to integrate the accounting of surface and groundwater by the end of 2008. WA: Western Australia’s State Water Plan is consistent with the NWI objectives in that it seeks accountability for surface and groundwater resources, with a priority given to resources under demand pressure. ACT: The ACT Government has already identified situations where close interaction between groundwater and aquifers and stream flow exist. NSW: Locations of significant interaction between groundwater and surface water sources were identified and mapped in July 2004. Broad identification completed. However, the extent and rate of interactions are not yet defined. Water plans should identify level of connectivity between surface and groundwater systems by 2010. NT: The Northern Territory is undertaking a range of studies to quantify groundwater and surface water connectivity. Once the connectivities are understood, the Northern Territory will incorporate them into integrated water accounting for connected systems. Qld: Interaction between groundwater and surface water is assessed during water resource planning processes on a catchment basis. SA: Establish a program to identify surface water and groundwater interactive systems by July 2007.

x) recognition of the connectivity between surface and groundwater resources and connected systems managed as a single resource

25 (ii) provide a statutory basis for environmental and other public benefit outcomes in surface and groundwater systems to protect water sources and their dependent ecosystems

Schedule E: Consideration in water plans to include an assessment of the level of connectivity between surface (including overland flow) and groundwater systems



NWI objective

NWI outcome

NWI action

Actions reported in NWI Implementation Plans Revise current water allocation plans to further recognise the interconnectivity between surface and groundwater, by July 2010. In comparison to other jurisdictions, the volumes of water associated with the interaction between surface water and groundwater is on a much smaller scale. The prime areas where there is interaction include the Mount Lofty Ranges, the Clare Valley and the Flinders Ranges, where groundwater provides stream base flow. Most of these baseflows are ephemeral but can result in residual permanent pools that sustain water dependent ecosystems. Following the prescription of Mount Lofty Ranges, technical work is being conducted to identify this interaction as part of the assessment of the capacity of the water resources, including the impact on water dependent ecosystems, and subsequent development of the water allocation plans. This technical work will ensure the maintenance groundwater discharge is provided for Tas: The Australian Government Water Fund Project ‘Better information for better results – enhancing water planning in Tasmania’ will provide understanding of the interrelation between key groundwater – surface water systems. Includes the development of models of groundwater-surface water hydrology. End date: Jan 2008. Vic: Ongoing investigations to determine areas with strong interconnections between surface water and groundwater. Developed legislation to enable integrated groundwater and streamflow management plans WA: Connection between surface water and groundwater resources will be investigated as part of the development of statutory management plans. Decisions on the level of modelling and assessment to define surface and (European Commission 2000) groundwater integration will be made in each case, depending on the hydraulic circumstances.



5.5 International groundwater policy: Europe
For this review, we thought it would be useful to provide some brief outlines of the groundwater policies currently underway in other parts of the world – partly for context but also to indicate potential sources of information or guidance for Australian work on SGDEs and to take some lessons from overseas experiences. The European Union (EU) Water Framework Directive (WFD) came into force in 2000 (2000/60/EC). Its aim is to achieve ‘good ecological and chemical status’ for water across the 27 EU member states by 2015. The WFD is based on the concept of river basin management. A river basin management plan to protect and improve water quality will be developed for each river basin, some of which transcend national borders. The WFD requires classification of water bodies into five quality classes using an Ecological Quality Ratio: the ratio between a reference condition and the measured status of a waterbody (see <>). A daughter directive to the WFD dealing with groundwater quality was adopted in 2006 (2006/118/EC). This establishes criteria for evaluation of good groundwater chemical and quantitative (water level) status, and aims to harmonise the monitoring and evaluation of groundwater quality across the EU. The WFD defines groundwater bodies as distinct volumes of groundwater within an aquifer or aquifers. Although the ecological status of groundwater bodies is not considered directly (Danielopol et al. 2004), assessment of groundwater chemical status requires assessment of the interactions between groundwater and surface waters, and analysis of the impact of groundwater bodies on the ecological status of surface water bodies and terrestrial GDEs. Further, the groundwater directive states (paragraph 20 of the recital): ‘Research should be conducted in order to provide better criteria for ensuring groundwater ecosystem quality and protection. Where necessary, the findings obtained should be taken into account when implementing or revising this Directive. Such research, as well as dissemination of knowledge, experience and research findings, needs to be encouraged and funded’ (see <­ framework/groundwater/policy/current_framework/index_en.htm>). The objectives of the WFD that relate to groundwater are as follows: • • • • achievement of good groundwater quantitative and chemical status by 2015 prevention of deterioration from one status class to another (for example, prevention of pollution) reversal of any significant and sustained upward trends in pollutant concentrations and prevention or limitation of input of pollutants to groundwater achievement of water-related objectives and standards for protected areas.

Lessons from the European experience Common conceptual models and terminology
Conceptual models have been developed for processes in groundwater bodies using a source-pathway-receptor paradigm (Figure 6). For each groundwater body, anthropogenic activities are identified that could exert an environmental effect or pressure. This is analogous to the concept of threatening processes. The risk for each groundwater body is assessed by identifying the pathways between pressure and receptors such as an aquatic ecosystem or a water user. The level of vulnerability is determined from the horizontal and vertical distance between pressure and receptor, and characteristics of the groundwater body such as residence times, porosity, transmissivity and hydraulic gradient. Krause et al. (2007) apply this approach in developing an ecohydrogeological framework to assess the risk of significant damage to groundwater dependent terrestrial ecosystems in the United Kingdom and the Republic of Ireland.



Figure 6: Conceptual model of anthropogenic impacts on groundwater bodies
water user receptor aquatic ecosystem receptor

pollution source

direction of groundwater flow

An anthropogenic impact produces a pressure that is transmitted along a groundwater pathway to receptors. The pressure is diluted or attenuated (reducing size of arrows) along the pathway. Properties of the aquifer determine the extent of dilution or attenuation. Adapted from Quevauviller (2004).

Groundwater bodies are categorised in the EU approach as being at significant risk, probably at significant risk but more information is needed, probably not at significant risk, and not at significant risk. This risk assessment determines the research, monitoring and management priorities. The effects of climate change on water quality parameters could oblige re­ evaluation of reference conditions and restoration targets (Noges et al. 2007). As well as helping guide risk assessment and management, these models ensure that there is shared understanding and agreement on pollutant pathways and processes within groundwater bodies. Use of common terminology based on the shared conceptual models greatly assists communication and development of useful knowledge structures (Benda et al. 2002).

5.6 International groundwater policy: South Africa
South Africa’s National Water Act 1998 provides for a reserve to be set aside for essential human use and to protect aquatic systems before water is allocated to other uses. Water resources are defined in the Act as including watercourses, surface water, estuaries and aquifers, so ostensibly groundwater and surface water are afforded the same provisions. Nevertheless, like Australia, omission of explicit inclusion of groundwater in the ecological reserve allows it to be disregarded (for example the exclusive attention to rivers by van Wyk et al. (2006)), lack of procedural clarity hampers implementation of ecological protection for GDEs (MacKay 2006), and investigations of groundwater dependence have focussed on terrestrial ecosystems (Le Maitre et al. 1999). A recent report (Colvin et al. 2007) summarises knowledge of GDEs in South Africa, identifies knowledge gaps, and makes recommendations for further research to meet the requirements of the relevant legislation.



6 Knowledge needs and research directions
The knowledge needed to meet the agreed objectives of the NWI and specific research questions to provide these data are outlined in Table 6. Accompanying policy actions (Box 13) are needed to support these research directions. The greatest benefit of groundwater ecology to groundwater management derives from the identification of ecosystem and habitat types, with application to conservation planning, design of monitoring programs and sustainable use (Danielopol et al. 2008). Because many surface water ecosystems are interdependent with SGDEs, the water needs of SGDEs must be considered in water planning. Similarly, ecosystem functions of SGDEs must be maintained, if only to meet desired environmental outcomes for surface waters. Specific research directions are discussed in the following sections. Box 13: Necessary policy actions Necessary policy actions are as follows: • • • • revise the National Principles for the Provision for Water to Ecosystems (ARMCANZ/ANZECC 1996) to take account of groundwater agree on nationally-consistent sampling, monitoring and reporting protocols for SGDEs improve frequency and extent of groundwater level and water quality monitoring establish mechanisms to facilitate sharing of information, case studies and methods, for example, through workshops, publications and websites such as the Bureau of Rural Sciences ‘Connected Waters’ website support regular workshops for water managers, consultants, and taxonomists to develop rapid assessment tools, identify priorities for research and develop funding proposals require lodgement of specimens in a centralised register or ‘Stygobase’ that conforms to a standard, nationally-agreed terminology and including metadata such as sampling method, frequency of sampling, details of aquifer type and other location data including associated water quality data such as dissolved oxygen and conductivity establish coordinated data management and storage procedures require that determination of EWRs and EWPs for groundwater consider the environmental values and water quality objectives established under the National Water Quality Monitoring Standards for connected surface waters.

• •

• •



Table 6: Knowledge needed to address NWI objectives, and suggested research questions
NWI objective iii) statutory provision for environmental and other public benefit outcomes, and improved environmental management practices Broad knowledge needs Improved ecological understanding of SGDEs and of the relationship between biodiversity and ecosystem function and the provision of groundwater ecosystem goods and services Water management arrangements will maintain ecosystem function, water quality, and biodiversity values Specific research questions Can the proposed typology of groundwater habitats be incorporated into subdivisions of
groundwater management units to develop biologically relevant management units?
What are the drivers of SGDE ecosystem function? How consistent are these drivers across
functional units in our typology and across time?
What are the faunal or environmental variables or suites of variables that indicate changes and
predict trends in ecosystem function? What is their reliability?
What are the threshold values in indicators that trigger management action?
Do changes in wetting and drying cycles affect the functioning of aquifer biofilms?
Does stygofauna have a role in maintaining hydraulic conductivity and stimulating biofilm
function, and in bioremediation?
Are rates of decomposition of organic matter similar in SGDEs with similar geology and
groundwater reserves?
What level of taxonomic identification is sufficient for monitoring (hinges on research question)?
Conservation priorities Undertake targeted surveys to fill knowledge gaps regarding: the range of short range endemics, rare species, key species of particular evolutionary significance, or which are key ecosystem service providers; representative communities; identification of drivers of SGDE community ecology and ecological processes. What are the indicators and predictors of high conservation value for SGDEs and their recharge sites? Investigate methods such as phylogenetic diversity (Forest et al. 2007) to help identify conservation priorities. Take account of climate change Use the typological approach to identify which SGDEs are at highest risk from climate change. Consider strategies to protect vulnerable SGDEs, especially those providing key goods and services.



NWI objective iv) complete the return of all currently overallocated or overused systems to environmentally-sustainable levels of extraction

Broad knowledge needs Determination of environmentally sustainable extraction Processes of recovery for groundwater systems Restoration strategies for SGDEs, including effects of restoration of adjacent terrestrial and surface aquatic ecosystems

Specific research questions Monitor faunal community and water quality variables in areas where extraction is occurring.
Analyse correlations and generate hypotheses for field testing.
Test definitions of sustainability of groundwater extraction by monitoring changes in biotic and
water quality indicators.
Determine acceptable limits of change in groundwater regime.
Monitor capacity for stygofauna recovery after overextraction has been corrected.

vii) water accounting which is able to meet the information needs of different water systems in respect to planning, monitoring, trading, environmental management and on-farm management

Methods for measuring indicators of biodiversity, ecological processes and ecosystem services in SGDEs Protocols for data recording, storage, analysis and reporting Establishment of database that meshes with databases on surface biota and environmental variables

Compare methods of data collection, storage and analysis. Look overseas for current approaches to data base management (for example, PASCALIS). Link proposed ‘Stygobase’ with existing GDE register.

x) recognition of the connectivity between surface and groundwater resources and connected systems managed as a single resource

Identification of indicators of significant interconnection between groundwater and surface water for the functional units in our typology

Compare indicators of interconnection between groundwater and surface water (conservative tracers, temperature, fauna, water quality variables). How are aquifer processes linked with quality and quantity of discharges to dependent ecosystems? Coordinate studies investigating processes and impacts in SGDEs and connected systems. How does management action, including EWPs, in connected systems impact on SGDEs? Are responses confined only to the ‘highly connected’ systems in our typology?



6.1 What is the appropriate management scale for SGDEs?
An ecological view of groundwater as habitat and as providing ecosystem goods and services raises the question of appropriate management scale. Until the water reforms of the last decade, groundwater management in Australia was not concerned with ecological considerations such as the water needs of GDEs. To accommodate the requirement of the water reforms that water planning provide for environmental outcomes including the maintenance of ecosystem function, a smaller, ecologically-relevant scale of management unit is needed. Yet, although effective management must focus at the ecosystem scale, the national groundwater management unit is far larger. The Australian Water Resources 2005 (National Water Commission 2006) uses the groundwater management units designated by the National Land and Water Audit (Figure 7). The groundwater management unit is a hydrogeological unit defined as an area with appropriate scale for groundwater management practices dealing with resource issues and intensity of use (National Water Commission 2006). Although we recognise that the Australian Water Resources 2005 was a first step and we acknowledge that the authors were constrained by the existing planning framework, the information presented in Appendix C and Map 45 (reproduced here as Figure 7) of the AWR 2005 Baseline Assessment Level 1 Key Findings Report has little practical application for planning due to its extremely coarse scale. Figure 7: The extremely coarse scale of identification of GDEs within groundwater management units in the Australian Water Resources 2005 assessment

In practice, groundwater is not managed at the scale of the groundwater management unit but at smaller-scale planning units variously termed water control districts (Northern Territory), regional groundwater management areas (Western Australia), water resource management areas (Victoria), water resource plan areas (Queensland), water management areas (Australian Capital Territory, Tasmania), and prescribed wells areas (South Australia).



In South Africa, a groundwater management unit is defined as ‘an area of a catchment that requires consistent management actions to maintain the desired level of use or protection of groundwater’ (Parsons and Wentzel 2007). This seems to be a good way forward.

6.2 A proposed typology of SGDEs
For the purpose of ecologically-relevant groundwater management in Australia, we propose the development of a classification or typology of SGDEs based on descriptors of habitat. This typology would help to simplify a diverse array of habitats and might even generate predictions of the ecological traits that might characterise the fauna in these types. For example, Claret et al. (1999b) classified subsurface faunal communities using species traits derived from research in Europe, sorting subsurface invertebrates according to their degree of affinity to the subsurface habitat, and showing that the proportions of these categories changed with different habitat conditions. In an analogous approach, Timms and Boulton (2001) derived a typology for central Australian arid zone floodplain wetlands based on correlations between invertebrate composition and the driving variables of water regime, salinity and turbidity within and among wetland types. The main abiotic controls on animal distributions are ecological factors determining the availability of resources such as food (energy) and living space (habitat). In SGDEs, resource availability is determined broadly by groundwater environment type; geology determines the porosity and contributes to the hydraulic conductivity of the aquifer matrix. But aquifer type alone is insufficient. A hydrogeological typology would place two aquifer systems in the same category, but differences in climate and hydrologic connection (Box 14 and 18) are likely to drive major differences in ecosystem metabolism and faunal community characteristics. As another example, Schmidt et al. (2007b) found that stygofaunal assemblage composition did not reflect geological, chemical or topographical features in an alluvial aquifer in the Marbling Brook catchment near Perth, Western Australia, but was better characterised by a range of finer-scale abiotic features including dissolved oxygen and temperature. It is accepted that flow regimes in surface waters determine physical habitat and are a major determinant of biotic composition (Poff et al. 1997, Puckridge et al. 1998, Bunn and Arthington 2002). Similarly, the physical structure of an aquifer and the movement of water and allochthonous (externally sourced) materials through it largely govern the composition of its stygofauna (Strayer 1994). Groundwater upwelling zones in streams are characterised by low levels of dissolved oxygen (Malcolm et al. 2005); upwelling and downwelling zones are often dominated by different groups of fauna, with stygofauna and benthic species preferentially occupying groundwater and surface water respectively (Dole-Olivier and Marmonier 1992, Dole-Olivier et al. 1994, Malard et al. 2003, Sliva and Williams 2005). Porosity also determines the distribution of fauna by shaping the available physical spaces; in a fractured rock aquifer, fauna were distributed throughout the dendritic system of interconnected joints and fissures (Malard et al. 1996). Thus geomorphology, in particular interstitial space, is a driver of distribution and abundance of groundwater fauna (Dole-Olivier and Marmonier 1992, Rouch 1992, Ward et al. 1994, Rouch and Danielopol 1999), not only because it imposes spatial constraints (Creuzé des Châtelliers et al. 1994), but also because it influences the availability of nutrients and oxygen. Dominantly intergranular flow, intergranular/fracture flow, dominantly fracture flow or conduit flow determine whether flow is undifferentiated, through preferential pathways, or channelled through discrete pathways. This, in turn, determines the rate of transport of solutes and particulate matter, the rate of interchange of gases, and the spatial distribution of loci of biogeochemical activity thereby creating resource patches that drive the spatial distribution of fauna. Clearly, an ecologically-relevant classification of stygofaunal habitat would require a much finer spatial scale than that of the groundwater management unit to take account of smallscale differences in recharge and hydraulic conductivity. These local-scale effects influence the supply of organic material, which is the basis of many subsurface food webs (Datry et al. 2005, Hancock et al. 2005). Therefore, a spatial and temporal perspective that matches the tenets of modern groundwater ecology is needed. In a management context, a typology based on an ecological perspective could potentially help predict stygofaunal biodiversity, abundance and community structure (Hahn and Fuchs submitted) and would therefore be



useful in determining priorities for stygofaunal surveys and other management applications such as predicting species distributions, assessing vulnerability to risks, and identifying conservation priorities (Castellarini et al. 2007a, Castellarini et al. 2007b). Given our current lack of knowledge of Australian stygofauna, this typology could also reveal potential hot spots of biodiversity that need protection during groundwater resource development.

Box 14: Case study 2: An alluvial aquifer in temperate Australia – The Peel alluvium, NSW
Location: 31° 18’ S, 151° 09’ E Area: 196 square kilometres Maximum thickness of alluvium: 15–20 metres Composition: mainly sands and gravels Estimated porosity: 10 per cent

The Peel River, north-eastern NSW, is a 320-kilometre-long inland-flowing river. It joins the Namoi River, a major tributary of the Barwon-Darling system, west of Tamworth. Its width is restricted in the upper part of the valley, but below Tamworth the river flats reach their maximum width of more than three kilometres (Water Conservation and Irrigation Commission NSW 1970, Water Resources Commission 1986). Alluvium beneath the river flats contain an estimated 10 to 20 megalitres of groundwater per hectare (Peel and Upper Namoi Valley Irrigation Project Team 1989). The economy of the valley is supported by water from the Peel River and its alluvium. Chaffey Dam (capacity 62,000 megalitres, 43 kilometres upstream of Tamworth) provides water for irrigation and Tamworth city water supply (Peel and Upper Namoi Valley Irrigation Project Team 1989). Water in the Peel alluvium generally contains less than 1000 milligrams per litre total salts, attributable to ready recharge by rainfall and streamflow. Hydrological connectivity between the river and the alluvium is inferred from correlations between rainfall, streamflow and variations in water levels and bore yields (Water Resources Commission 1986). Before regulation, flows in the Peel River varied widely from periods of no flow to periods of overbank flooding. In the 45 years between 1923 and 1968, flows varied from about five to 450 per cent of recorded annual average flow (Water Conservation and Irrigation Commission NSW 1970). Streamflow records indicate that all streams in the valley have ceased to flow for extended periods of time during droughts; the longest period without flow was 223 days from January to August 1966 for the Peel River at Piallamore (Water Conservation and Irrigation Commission NSW 1970). Considerable declines in the watertable were experienced during drought periods, necessitating the deepening of some wells (Water Conservation and Irrigation Commission NSW 1970). The frequency of no-flow conditions was a major restriction on farming development in the Peel Valley, prompting the construction of Chaffey Dam (Water Conservation and Irrigation Commission NSW 1970). Since 1925, about 40 floods have exceeded the trigger level for flood warnings at Tamworth (Bureau of Transport Economics 2001). The longest interval without floods of this magnitude was 1925 to 1931. The most severe sequence of floods occurred from 1950 to 1956, when there were twelve floods that exceeded the trigger level (Water Conservation and Irrigation Commission NSW 1970). Regular inundation of river flats would have provided nutrients as well as connectivity to the aquifer, and it is clear from the stream gauge records that water level fluctuations in the hydrologically-connected Peel alluvium were an ecosystem characteristic. The NSW Department of Land and Water Conservation’s Stressed Rivers Report (1998b) listed the Upper Peel River as a category S3 (high) in overall stress classification, a high hydrology stress rating and a medium environmental stress rating, indicating that water extraction is likely to be contributing to environmental stress and that the river was a high priority for the preparation of a river management plan. In a similar assessment of stressed aquifers, the Peel Valley alluvium was identified as being at high risk of over-extraction and a high priority for the development of a management plan (NSW Department of Land and Water Conservation 1998a). Regular quarterly surveys from September 2005 to October 2007 (Tomlinson, unpubl.) revealed an abundant and diverse stygofaunal community widespread throughout the Peel alluvium. Lack of data from before dam construction prevents assessment of how these patterns are modified from a reference state. This research is investigating relationships between water quality variables, water level fluctuations and temporal and spatial patterns of stygofaunal species distributions and community composition. The management challenge in the Peel valley is to provide for the consumptive uses of water from the regulated river and its alluvium while providing for the environmental water requirements of the aquifer ecosystem in which hydrological conditions are highly modified from the natural state.



Box 15: Case Study 2: An alluvial aquifer in arid Australia – Alice Springs Town Basin, NT
Location: 23° 41’ S, 133° 52’ E Area: 7.7 square kilometres Maximum thickness of alluvium: 25 metres Composition: a mixture of gravel, sand, silt and clay Estimated porosity: 20 per cent

The Alice Springs Town Basin is a small alluvial basin associated with the Todd River on which the town of Alice Springs is now situated (Northern Territory Government 2007). Until recently, it was recharged primarily from ephemeral flows in the Todd River. The Town Basin supports culturally important riverbed vegetation, including mature river red gums that have traditional significance to the local Arrernte people. Groundwater flows both underneath the Todd River and along buried former channel beds. Before the 1970s, water levels in the Basin fluctuated widely in response to episodic river flow. For some 50 years, the Town Basin was the main water supply to Alice Springs. Extraction virtually ceased in the 1970s following the development of a borefield accessing deeper sedimentary aquifers of the underlying Amadeus Basin. Subsequent high rainfall years and high recharge from irrigation of lawns resulted in sustained high water levels in the Town Basin, with levels remaining four to seven metres higher than those recorded before the establishment of the Amadeus borefield. These high water levels mobilised salts from fringing bedrock, resulting in dramatic increases in salinity of up to 7000 milligrams per litre total dissolved salts (Read 2003). The salinisation is also due to evaporation associated with recharge from lawn overwatering. Town Basin water is no longer potable, and although the Town Basin now supplies water for irrigation of lawns and the golf course, the quality in some parts of the Town Basin is now too poor even for this use. As well as higher salinity, water quality is affected by the urban and industrial activity (Read 2003). The Town Basin presents an interesting management challenge. It is a shallow, alluvial aquifer that, despite hydrological disturbance, salinisation and poor quality, continues to supply consumptive and non-consumptive uses, including groundwater dependent ecosystems. The Alice Springs Water Resource Strategy recommends that to maintain the health of the river red gums, groundwater levels in the river corridor must not decline beyond eight metres below ground level. An open research question is whether this imperative to protect the culturally-significant river red gums will also provide for the water needs of other groundwater dependent species. It is likely that there is a stygofaunal community of scientific interest in the Town Basin. The presence of stygofauna in the Town Basin was confirmed by preliminary sampling of three monitoring bores in September 2006, which revealed a parabathynellid syncarid (Tomlinson, unpublished data).

The necessity for a revised aquifer typology has been driven in Europe by the implementation of the Water Framework Directive (WFD). This involves characterising water bodies and types, identifying pressures and impacts on these waterbodies, assessing risks to waterbodies, and developing criteria to assess ecological and chemical status. The inadequacy of defined groundwater management units that might contain more than one aquifer and are not on a scale appropriate for ecological management had already been noted by Gibert et al. (1994). In response to the management requirements of the WFD, Dahl et al. (2007) proposed a multi-scale typology of groundwater-surface water interaction based on geomorphic, geological and hydrological concepts reflecting functional linkages and controlling flow processes at successively finer spatial scales. On a catchment scale (more than five kilometres), groundwater flow is classified by regional geomorphology: on an intermediate or reach scale (one to five kilometres), the groundwater-riparian interactions are classified by hydrogeology; and at the local scale of 10 to 1000 metres, classification is based on the type of local flow path, classified as either diffuse, overland, directly connected to groundwater, or through drainage ditches. Flow regime is important in delineating groundwater bodies and assessing their vulnerability to pollution. Vulnerability assessment involves considering the travel time of infiltrating water, the effectiveness of hydrological connection between surface and groundwater, and the hydrogeological attributes of the aquifer materials (Quevauviller 2008). These considerations are readily applicable to an ecologically-focused typology. Hahn (submitted) develops a scale-based, ecologically-focussed hierarchical typology of groundwater habitats. In this approach, communities are defined at a macroscale (continental) by biogeography, at the mesoscale (landscape) by the aquifer type, and at a local scale by the degree of hydrological exchange with surface water. The degree of



hydrological exchange determines the nutrient supply, rated as poor, moderate or good (Hahn 2006). Hahn and Fuchs (submitted) applied this approach to the identification of groundwater habitats in the south-western German state of Baden-Württemberg (an area of 37,750 square kilometres). The state was separated into regional geological units, which were subdivided into geohydrological groups (aquifer types). Stygofaunal community structure was found to be shaped broadly by the geohydrological type, and more finely by sub-types characterised by differences in porosity and hydraulic conductivity, which influenced hydrological exchange and the amount of living space. A typological approach is taken by Colvin et al. (2007) in their classification of ‘aquifer dependent ecosystems’ in different type-settings in South Africa. The type-settings are presented as a matrix of six aquifer types based on lithology and seven habitat types similar to the Australian GDE classes. This simplified type-setting enables a national-scale overview of the main aquifer types and assists identification of possible locations for aquifer dependent ecosystems. The authors use the term ‘aquifer dependent’ to avoid the confusion that can be generated by definitions of groundwater that include all water below the ground, rather than water within the saturated zone. Thus, they define aquifer dependent ecosystems as ecosystems that depend on groundwater in, or discharging from, an aquifer. A typology of SGDEs has not been developed for Australia. The European approach of hierarchical classification incorporating ecological factors is potentially useful, although its application must take account of differences between Europe and Australia, including the greater range and variability in environmental conditions in Australia. An ecohydrogeological approach to an Australian SGDE typology is suggested in Table 7. This classification is based on the amount of living space for stygofauna and resource supply, and it is intentionally focused on invertebrates; different classifications might be needed for microbial or other ecological components of SGDEs. Degrees of primary, secondary and tertiary porosity determine available living space and place physical constraints on faunal size and food particles (for example, organic matter). The type of porosity also affects the spatial distribution of fauna and influences the surface area available for bacterial colonisation. Permeability affects hydraulic conductivity and therefore the delivery rate of oxygen, particulate organic matter and solutes. Table 7: Suggested SGDE typology
Resource supply Variable GWR High connectivity Hyporheic zone, vadose zone in discharge areas in the arid zone

Living space

Stable GWR

Stable GWR Low connectivity Deep sedimentary aquifers

High connectivity Between sediment Unconsolidated particles (primary aoelian, alluvial and/or lacustrine porosity) clays, sands and gravels In fractures, cracks Some along bedding sandstones and planes, and solution other cavities (secondary sedimentary porosity) rocks In large voids (tertiary porosity) Some karsts, sedimentary rocks, basalt, carbonates

Outcropping Deep, fractured fractured aquifers aquifers, some calcretes in arid zone Some karsts, Deep caves limestones, some calcretes, lava tubes

Adapted from Fetter (2001), Wendland (2007), Hahn and Fuchs (submitted) and Hahn (submitted). SGDE type is determined by attributes of the groundwater regime, which are driven by patterns of recharge and discharge, hydraulic conductivity and hydrologic connection to recharge. Disturbance may alter the groundwater regime or connectivity and cause shifts in SGDE type, for example, a stable groundwater regime, low connectivity SGDE may shift to variable groundwater regime, low connectivity under the pressure of unsustainable extraction.

Resource supply is determined by the groundwater regime and the degree of hydrologic connection to recharge. The groundwater regime is composed of the three attributes of flow



or flux, level or pressure, and water quality (Box 2), with the addition of temperature to the latter attribute. The groundwater regime is affected by patterns of recharge and discharge, which in turn are driven by climate. The range of climatic types across Australia (Figure 8) and the high variability of rainfall and streamflow (Finlayson and McMahon 1998) are likely to be strong drivers of spatial and temporal differences in aquifer hydrology where connectivity to the surface is high.

Figure 8: Classification of major climate types in Australia

Source: 2005 Bureau of Meteorology data

Seasonality and variability in rainfall and temperature in zones of groundwater recharge determine the frequency and volume of recharge, fluctuations in groundwater level or pressure, and water quality variations. Inputs of allochthonous organic matter, the main energy source for most SGDEs, are governed by the nature of the hydrological connection with surface waters or recharge area. Exchanges with the surface, and hence the timing and quantity of food supply, are affected by longitudinal, lateral and vertical dimensions of connection as well as the dimension of time (Ward 1989, Humphreys 2006a). Lateral and vertical connection can be through the hyporheic zone to surface waters, longitudinal linkages to recharge zones upstream, diffuse catchment inputs by percolation, or through conduits or other pathways of preferential flow through the aquifer. Linear distance to the nearest surface waterbody is seldom a reliable measure of longitudinal or lateral connection due to the probable presence of preferential subsurface flow paths or impermeable layers. The vertical connectedness can be inferred from the depth below surface in the case of infiltration through the unsaturated zone, but similarly this depth is not always indicative of connection if overlying formations are of low permeability. These factors, which control lateral and vertical connectivity, vary on a fine scale. For each aquifer type in each climatic region, the inputs of allochthonous resources depend not only on factors of catchment size and subsurface porosity, but also on how fine-scale surface morphology directs drainage (Humphreys 2000b).



This proposed typology assumes heterotrophic metabolism based on allochthonous nutrient sources. An allochthonous base for the food chain is prevalent in subterranean habitats (Gibert and Deharveng 2002) although chemoautotrophy is significant in particular systems, such as the anchialine Bundera Sinkhole on the Cape Range peninsula in Western Australia (Humphreys 1999b), cave lakes on the Nullarbor (Subterranean Ecology 2007) and deep subsurface environments such as the Great Artesian Basin aquifers (Kimura et al. 2005). Por (2007) suggests that a deep subterranean chemoautotrophic biome continuous with anchialine systems and marine hot vents and cold seeps could provide an ecological explanation for the high taxonomic diversity of subterranean fauna; however, this is speculative. Because rates of chemoautotrophic production are slow (Chapelle and Lovley 1990), it is assumed here that autotrophy makes an insignificant contribution to most subterranean food webs. Continuing research effort will generate faunal and environmental data to test the usefulness of the suggested typology and further elucidate the variables that drive faunal community composition and that are related to the void characteristics, connectivity, and variability of groundwater regimes. As more data accumulate on the environmental conditions and community characteristics of groundwater fauna across a range of SGDEs, it could be possible to plot species response curves (Figure 9) and therefore identify key driving variables and the tolerance levels of stygofauna to changes in groundwater regime as a result of groundwater extraction or other disturbance. It is likely that faunal community responses to gradients in environmental variables are influenced by a number of these variables, and so further research is also required to identify associations between combinations of environmental and faunal community variables at a range of scales, and to develop stressor gradients for these combined variables. It should also be considered that the magnitude and rate of change in responses could vary with small shifts in critical variables, and might not be consistent over time (Bressler et al. 2006, Hering et al. 2006, Johnson et al. 2006). These data and analyses would assist in developing an ecologically-based SGDE typology, enabling managers to estimate the likely distribution and composition of groundwater communities and helping to identify and prioritise knowledge gaps. The European approach of categorising groundwater bodies is similar to that of our proposed typology in which aquifer type and resource supply, determined by climate and degree of hydrological connection, determine SGDE type.

6.3 Investigations of functional groups
A currently-active research area centres on the relationship between biodiversity and ecosystem function, and involves the concept of the ‘functional group’, which is a set of species having a similar role in ecosystem processes (Chapin et al. 1992). Proceeding from this is the question of functional redundancy (Schwartz et al. 2000), if several species play a similar role, does loss of one or more of these species alter ecosystem function? Investigations of functional groups of benthic and hyporheic invertebrates in freshwater and marine environments (Mermillod-Blondin et al. 2001, Mermillod-Blondin et al. 2002, Gerino et al. 2003, Mermillod-Blondin et al. 2003, Mermillod-Blondin et al. 2004b, Mermillod-Blondin et al. 2005a) show the variability of species effects and interspecific effects within functional groups (Michaud et al. 2005, Norling et al. 2007). Caliman et al. (2007), working with sediment and benthic invertebrates collected from a shallow freshwater lagoon in Brazil, observed a significant positive effect of benthic bioturbator diversity on flux of total dissolved phosphorus in experimental microcosms. Boulton et al. (2008) characterised functional groups of stygofauna in alluvial aquifers as ‘ecosystem service providers’, which are collectively responsible for services such as bioturbation, stimulating microbial activity through grazing, and organic matter decomposition. Localised loss of common or species-diverse taxa within each group of ecosystem service providers might be readily compensated for, but loss of rarer taxa might not be so easily accommodated, potentially leading to an impairment of ecosystem services.



Figure 9: Response curves For any biologically-relevant abiotic variable there is a range over which biological responses occur (Figure 9a)

Figure 9a Response curve for a typical animal, showing the tolerance range of a biological indicator, in this case metabolic rate, and maximum and minimum temperature tolerance (Clapham 1973)
Tolerance range Metabolic rate Minimum Temperature


Within the response curve there is a range for which the response is optimum (Figure 9b).

Figure 9b Response curves with a broad optimum (a) and narrow optimum (b) (Clapham 1973)



Field observations of species responses might reflect responses to gradients in single environmental variables, but in many cases do not (Figure 9c) due to the effects of responses to other environmental variables or to biotic factors such as inter-specific competition.

Figure 9c Observed (field) species response and the experimentally-derived response curve (dashed) for an environmental variable. Points represent the observed response of the species at different locations (Clapham 1973).

Species response

Gradient of environmental variable



6.4 What level of taxonomic identification is necessary?
The level of taxonomic identification required for some management decisions (Marshall et al. 2006) has not yet been assessed for subsurface fauna: for example, is family level identification sufficient to assess a community response to changes in groundwater regime, or are there ecologically-relevant differences in the responses of species? These questions do not negate the necessity for species-level identification for biodiversity conservation. Due to convergent evolution and the development in multiple lines of phreatomorphies, there might be no readily-apparent morphological differences between taxa (Proudlove and Wood 2003) so DNA analyses are frequently necessary (Finston et al. 2004, Finston et al. 2007) but should be carried out in tandem with morphological descriptions to help non-experts identify taxa where possible. In parts of Europe, the stygofauna are well known; for example most of the German crustacean stygofauna have probably been described (Dr Hans Jürgen Hahn, University Koblenz-Landau, Germany, pers. comm.). A centralised database developed as part of the PASCALIS project (Gibert et al. 2005) contains distributional and other details of groundwater biodiversity drawn from published records of stygobitic taxa from six European countries. A complete species inventory for Australia is unrealistic in the short term as the time, expertise and resources are not available in the immediate future (the next five years) to conduct comprehensive surveys and identify samples; but improvements can be made in the current piecemeal and reactive approach. Data from stygofaunal surveys are not centrally stored and many surveys are conducted to answer immediate, local questions related to resource use rather than the integrated and multidisciplinary research questions necessary to assist management decisions about conservation and sustainable use. Spot surveys that take a scattergun approach to sampling and omit environmental data do not provide an understanding of the drivers of patterns of species distributions, abundance and community composition. Given our current poor knowledge of stygofaunal species occurrence and distributions, data are needed in order to identify appropriate criteria and indicators of biodiversity in SGDEs and to develop monitoring programs. Co-ordinated, well-planned and targeted research is needed to generate the data and analyses with predictive capacity that are meaningful for managers, and will also help the community understand the trade-offs implicit in water management decisions.

6.5 Measuring biodiversity and monitoring management action
A key management question is how to measure biodiversity and thus monitor the effects of management actions. There are two broad approaches to estimating biodiversity: use of taxon-based indicators, such as particular indicator species, and use of spatial or other features of community structure, such as habitat heterogeneity or species composition (Lindenmayer et al. 2000). Indicators are more than a means of estimating or monitoring biological diversity; they are most useful as tools to guide decision-making in policy. Identification of appropriate indicators is crucial to the application of basic science to natural resources management (Failing and Gregory 2003). A promising approach is the use of phylogenetic diversity (Forest et al. 2007). This is a biodiversity index that measures the length of evolutionary pathways that connect a given set of taxa and may be more useful than taxon richness in guiding conservation effort. Selecting the appropriate indicators enables managers to detect changes due to disturbance; using indicator response curves that have been derived experimentally or from field records gives managers some predictive capacity. The challenge in many groundwater environments is that the long residence time of groundwater creates a hydraulic time lag between disturbance and impact, and this can be exacerbated by an ecological time lag before change is detectable in species with longer life cycles and lower fecundity (Table 1). Presently, we have little idea of the shape of these species response curves for any groundwater taxon in the world, severely restricting the utility of any individual stygofauna species as an indicator.



6.6 Priority research directions
Our knowledge gaps about groundwater and SGDEs suggest broad questions (Box 16), which are addressed by specific research directions: • • determine the minimum level of taxonomic identification required to distinguish ecologically-relevant morphotaxa for management needs undertake surveys to investigate correlations between individual and suites of environmental variables (water quality variables, water level or pressure) with stygofaunal community composition and abundance, in different aquifer types (Henry and Danielopol 1998, Datry et al. 2005, Hahn 2006, Schmidt et al. 2007b) to derive species response curves that will build predictive capacity and help in conservation planning (Ferreira et al. 2007) such as formulating restoration actions apply survey results to extending our ecohydrogeological typology of stygofaunal habitats to enable identification of SGDE habitat types within groundwater management units at a scale appropriate for management compare species response curves within and between habitat types (Masciopinto et al. 2006) to derive type-specific stressor tolerance values (Bressler et al. 2006) and to identify tipping points (Nina Bate, EPA Victoria, pers. comm.) identify the key ecosystem service providers either at species, higher taxonomic group or functional group level and characterise their functional relationships and functional structure, assess how aspects of the community structure of ecosystem service providers and its changes affect provision of services, identify how key environmental factors affect ecosystem service providers and their provision of services, and measure the spatio­ temporal scales over which ecosystem service providers and their services operate (Boulton et al. 2008) focus taxonomic attention on developing molecular and morphological phylogenies for key groups that have potential as indicator taxa or key ecosystem service providers improve understanding of the effects of water quality changes (especially in electrical conductivity, temperature, and concentrations of nutrients and dissolved oxygen) on ecological processes to generate hypotheses of ecosystem processes and functions to be tested in field and laboratory experiments develop conceptual models of SGDE function to help identify indicators, design research and monitoring programs, assess resilience of SGDEs and identify, assess and manage risk, particularly the risk of a shift in SGDE type, for example a shift from a stable groundwater regime to a variable groundwater regime identify SGDEs at greatest risk from threats including climate change evaluate the 14 tools in Land and Water Australia’s toolbox (Clifton et al. 2007) for applicability in assessing the environmental water requirements of SGDEs. For example, tool 14 is ‘analysis of aquatic ecology’ or the use of ecological survey techniques to identify aquatic species with reproductive behaviour or habitat requirements that indicate groundwater dependency. An indicator identified for this tool is the presence of obligate groundwater fauna in the hyporheic zone. By extending sampling to bores in the connected alluvium, this tool can readily be applied to assessment of SGDEs and would provide valuable data to assist in management of the linked systems improve understanding of groundwater–surface water linkages and link aquifer processes with quality and quantity of groundwater discharges to dependent ecosystems develop approaches to rescaling models of aquifer processes from the hydrogeologic to an appropriate ecological scale (similar to the challenge of downscaling global climate data for regional applications); investigate how fine scale patterns of discharge and rates of salinisation vary with topography (Doble et al. 2006)

• •

• •

• •



develop a definition of ecosystem health in SGDE types based on type-specific indicators of biodiversity and water quality, and including limits of acceptable change in these indicators and triggers for management actions develop a framework for identifying high conservation value in SGDE types, identify areas with high biodiversity value, areas that are most heavily impacted, and areas that are vulnerable to loss of biodiversity value derive priorities for protection or restoration effort by identifying areas already impacted or under pressure which would most reward conservation or restoration effort (Linke and Norris 2003) using an approach that considers irreplaceability, condition and vulnerability (Linke et al. 2007) develop management practices that optimise consumptive use of SGDE goods in the context of climate change and maintenance of ecosystem services revise threshold values for limits on contaminant levels in groundwater (Hose 2005, 2007).

• •

Box 16: Understanding the groundwater resource What are the characteristics of the groundwater regime (flow/flux, level/pressure, water
What is the water balance (location, rate and volume of recharge and discharge)?
What are the water access entitlements and when are they exercised?
What SGDEs are present? What are the characteristics of subsurface biodiversity and
ecosystem services? How are they related?
What are the environmental water requirements?
What are the indicators of ecosystem condition and what are the acceptable levels of change
in these indicators?
What are the risks to the resource, including land uses, extraction, climate change, and
threats from connected ecosystems?
What is the sustainable level of extraction? How does it change over time?
What actions are necessary to protect biodiversity and ecosystem services including provision
of goods?
Adapted from Cullen (2006)
Presently reference condition data are scanty because surveys are constrained to the existing bore network, which was established to monitor the impacts of groundwater extraction. A riskbased approach will identify aquifer habitats that are under pressure and have not been sampled adequately: so far the effort has focused on some calcrete, alluvial and karstic habitats and aquifers in mineraliferous rocks subject to mining. Sampling other habitat types could elucidate ecological questions such as the function of ecotones and the role of less porous aquifers as faunal habitat. Within-habitat sampling should be stratified (Castellarini et al. 2007a). Consideration should be given to evaluating existing aquatic research projects for opportunities to collect and synthesise data that may be relevant to SGDE management. Examples include projects determining the environmental water requirements of linked GDEs, assessing the impact of regulation, surface water extraction and environmental flow releases in rivers with hydraulically connected alluvium, and projects where opportunities exist for stygofaunal and water quality monitoring during aquifer injection and artificial recharge, groundwater bypass during mining or construction projects, assessments of aquifer water balances or economic valuation of aquifer goods and services. For sustainable management of groundwaters and connected surface waters there must be cross-disciplinary research and management. Coordinated analysis of physico-chemical, faunal and hydrological factors will assist the development of practical, on-the-ground solutions to management needs.



Agencies and research groups should be encouraged to identify challenges to integration, develop and share strategies to address these challenges, and promote joint work, by: • • supporting and publishing case studies of projects in which hydrogeological and ecological research questions were integrated explicitly in the study design holding joint workshops between hydrogeologists and both terrestrial and aquatic ecologists in which disciplinary axioms and conceptual models are shared, assumptions are identified, research questions are explored and formulated jointly, and the barriers to effective cross-working are worked through encouraging joint or cross-publication, especially between hydrogeologists and ecologists maintaining up-to-date websites that report on work in progress, minimise duplication of effort and ensure ready availability of data.

• •



7 Conclusion

This review demonstrates extensive knowledge gaps about the distribution, composition and biodiversity value of Australian stygofauna, and the rudimentary level of our understanding of the drivers of subsurface ecological processes. It also demonstrates that many 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. Disturbance such as pollution or management interventions either in SGDEs or connected systems has flow-on effects, often with time lags. We propose an ecologically-oriented typology of SGDE habitats that will assist in developing research projects that are most likely to meet the environmental water objectives of the NWI. The research directions identified here aim to produce decision tools and develop standard methods and protocols for monitoring and assessing indicators of SGDE health and identifying high conservation value ecosystems, and to provide guidance on SGDE-specific management actions to maintain biodiversity, ecosystem function and water quality.



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Aeolian Allochthonous Relating to or arising from the action of wind Originating outside the ecosystem under discussion (Boulton and Brock 1999) Bodies of saline water with subterranean connections to the sea and restricted openings to the open air, showing marine and terrestrial influences (Iliffe 2000) Derived from human activities A geologic unit that can store and transmit water at rates fast enough to supply reasonable amounts of water to wells (Fetter 2001) A geological layer of low permeability than can store groundwater and also transmit it slowly from one aquifer to another (Fetter 2001) The variability among living organisms from all sources, including terrestrial, marine and other aquatic ecosystems and the ecological complexes of which they are part; this includes diversity within species (genetic), between species, and of ecosystems An area featuring exceptional concentrations of endemic species and experiencing exceptional loss of habitat (Myers et al. 2000) Carbonate deposits that form in soil or in the vicinity of the watertable as a result of evaporation of soil water or groundwater respectively Rocks consisting primarily of a carbonate mineral such as calcite (CaCO3) or dolomite (CaMg(CO3)2), the chief minerals in limestone and dolostone respectively The loss of water from groundwater to surface water, the atmosphere and the ocean. Includes springs, diffuse seepage into drainage systems (both natural and anthropogenic) and lakes, diffuse and localised discharge through the seafloor, evaporation of soil moisture that is replenished by seepage (dry salt lakes) and transpiration by phreatophytic vegetation that draws its water from the watertable (UNESCO/IHP 2006) A transition zone between two ecosystems (Brewer 1988) The water regimes provided as a result of the water allocation decision-making process taking into account ecological, social and economic impacts The water regime needed to maintain ecological values and ecosystem services of water dependent ecosystems at a low level of risk (SKM 2001) The heterogeneous interface between unconsolidated material and solutionally altered carbonate rock, which is partially saturated and capable of delaying or storing and locally rerouting vertical infiltration to the underlying karst aquifer (Jones et al. 2004)

Anchialine habitats

Anthropogenic Aquifer



Biodiversity hotspot


Carbonate rocks


Ecotone Environmental water provisions (EWPs)

Environmental water requirements (EWRs) Epikarst




The enrichment of water bodies with excess nutrients, typically nitrogen and phosphorus, and the subsequent effects on water quality and biological structure and function. It is a process rather than a state (Rast and Thornton 1996) Rate of groundwater flow per unit width of aquifer

Flux (in hydrogeological terms) Groundwater (hydrogeological definition) Groundwater, (ecological definition)

The subsurface water that occurs beneath the watertable in soils and geologic formations that are fully saturated (Freeze and Cherry 1979)

Water that has been present in pores and cracks of the saturated zone of soil or rock for sufficient periods of time to undergo physical and chemical changes due to interactions with the aquifer environment An ecosystem that would be significantly altered by a change in the chemistry, volume and/or temporal distribution of its groundwater supply (Parsons and Wentzel 2007). The degree of ecosystem dependence on groundwater is proportional to the fraction of the annual water budget that ecosystem derives from groundwater (Hatton and Evans 1998). The underground pathway by which ground water moves from areas of recharge to areas of discharge A hydraulically connected groundwater system that is defined and recognised by Australian State and Territory agencies. This definition allows for management of the groundwater resource at an appropriate scale at which resources issues and intensity of use can be incorporated into groundwater management practices. In South Africa a GMU is an area of a catchment that requires consistent management actions to maintain the desired level of use or protection of groundwater; delineation is based on management considerations rather than geohydrological criteria (Parsons and Wentzel 2007)

Groundwater dependent ecosystem (GDE)

Groundwater flow system Groundwater management unit (GMU)

Groundwater regime (GWR)

The three broad attributes of groundwater that are ecologically significant to dependent ecosystems: flow or flux, level or pressure, and water quality The period of time from when a groundwater parcel percolates into an aquifer at a certain site to its outflow into surface water (river, lake, sea) A rate of flow indicating the ease with which water will pass through aquifer material The water-mediated transfer of matter, energy, and/or organisms within or between elements of the hydrologic cycle The saturated interstitial areas beneath the stream bed and into the stream banks that contain some proportion of channel water or that have been altered by channel water infiltration (White 1993) The fauna occupying the hyporheic zone

Groundwater residence time

Hydraulic conductivity Hydrologic connectivity Hyporheic zone





A Slovenian word describing a terrain characterised by sinkholes, caves and springs developed most commonly in carbonate rocks where significant solution of the rock has occurred due to flowing water (Jennings 1985, ‘Culver et al. 1995, ‘Fetter 2001) Strips of buried sand and gravel laid down by former water courses The property of porous materials which determines the flow of fluid under pressure; it is a function of porosity and the interconnectedness of the pore spaces The convergent morphological, behavioural and physiological features of stygobites (Humphreys 2000a) The percentage of the aquifer matrix that is taken up by space, comprising pores between grains (primary porosity), fractures (secondary porosity) and enlarged cavities (tertiary porosity) The sandy zone on the shore of a surface water body between the highest water level and the lower limits of submersed rooted vegetation (Wetzel 2001) Landforms which resemble karst but are not produced by solution of rock but by processes such as wave action, earth movements or the evacuation of lava (Halliday 2007) Any influx of water entering a groundwater system at any of its defined boundaries. Includes natural recharge by diffuse infiltration, subsurface preferential flow and inflow from streams and lakes, and artificial recharge from intentional aquifer storage and excess irrigation (UNESCO/IHP 2006) Aquatic animal which completes its life cycle in groundwater Aquatic animals found in groundwater; sometimes used as a synonym of stygobite Animals which spend part of their life cycle in groundwater Animals which occur accidentally in groundwater but have no affinity with groundwater habitats An 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 groundwater supply (Adapted from Parsons and Wentzel (2007)) A measure of the amount of water that can be transmitted horizontally through a unit width by the full saturated thickness of an aquifer under a hydraulic gradient of 1 (Fetter 2001) Terrestrial animals living in caves and other air-filled subterranean spaces Classification of habitats into types defined by ecological descriptors The unsaturated zone between the watertable and the land surface

Palaeochannels Permeability






Stygobite Stygofauna

Stygophile Stygoxene

Subsurface groundwater dependent ecosystem (SGDE) Transmissivity


Typology Vadose zone



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