This essay briefly reviews perceived values of stygofauna and benefits of their inclusion in hydrogeological surveys of groundwater, and summarises the legislative and policy framework for stygofaunal surveys. Although focused on Australia, the issues discussed are of broad, international concern. A staged approach to surveys is advocated where investigations progressively increase in complexity. This aims to overcome the current paradox of omitting stygofauna from groundwater monitoring because there is insufficient information for the interpretation of survey results — yet, if stygofauna are not sampled, then the information will never be collected to address the knowledge gaps.

Although we are still developing our understanding, there is increasing recognition that groundwater is essential to many ecological communities. Groundwater is a connector, not just in the aquifer itself, but within, across, and between surface waters and many terrestrial ecosystems. Where the water table intersects or comes close to the land surface, contributions of water and nutrients to plant roots and aquatic ecosystems can be critical to their persistence. Consider that precipitation is the dominant source of water in nearly all wetland systems, yet the influence of the lesser groundwater flow component can be sufficient from an ecological perspective to yield an entire new type of wetland, the fen. Influxes of groundwater to lakes, rivers, and wetlands can change whole-system physico–chemical properties such as temperature and salinity, while also providing more subtle influences on microenvironments and their ecological processes. Infiltration of water from surface aquatic ecosystems and rainfall can have an equally significant effect on aquifer ecology, especially on microbes and subsurface invertebrates. Whether water is flowing into or out of an aquifer, or is moving from one part to another, it is the extent and intensity of connectivity that often determines its importance to ecosystems. Moreover, the same location in space can have all three types of flows at different periods of time. Surface ecological processes (such as evapotranspiration) can significantly impact hydrological responses and related hydrochemical function. Thus, the relation of groundwater hydrology to patterns and processes in ecology is a 'two-way street' where understanding the feedback of one to the other serves as a powerful lens through which to evaluate and explain the functioning of natural ecosystems.

Many rivers are classified as groundwater-dependent ecosystems (GDEs), owing to the contribution of groundwater to their base flow. However, there has been little explicit recognition of the way groundwater influences riverine biota or processes, how degrees of ecological dependency may vary, and the management implications ofthis dependency. The permeable beds and banks of these GDEs where surface water and groundwater exchange are termed 'hyporheic zones'. They are often inhabited by invertebrates, with varying reliance on groundwater, although the ecological roles of these invertebrates are little known. Upwelling hyporheic water can promote surface primaryproductivity, influence sediment microbial activity, and affect organic matter decomposition. In many intermittent streams, variable groundwater inputs alter the duration of flow or water permanence, and the duration and timing of these largely govern the biota and rates of many ecosystem processes (e.g. leaf decomposition). Not only is the physical presence of water important, thermal and chemical conditions arising from groundwater inputs also have direct and indirect effects on riverine biota and rates or types of in-stream processes. Differing degrees of dependency of rivers on groundwater mediate all these influences, and may change over time and in response to human activities.Alteration of groundwater inputs through extraction from riparianwells or changes in localwater table have an impact on these GDEs, and some current management plans aim to restrict groundwater extraction from near permeable river channels. However, these are often ‘blanket’ restrictions and the mechanisms of GDE dependency or timing of groundwater requirements are poorly understood, hampering refinement of this management approach. More effective management of these GDEs into the future can result only from a better understanding of the mechanisms of the dependency, how these vary among river types and what in-stream changes might be predicted from alteration of groundwater inputs.

1. Growing recognition of the ecological significance and biodiversity of groundwater fauna in Australia has led to statutory requirements for monitoring these communities prior to resource development. However, the efficiency of methods for assessing community composition and taxa richness remains untested, hampering the collection of reliable data for compliance. 2. We assessed the efficiency of two commonly-used methods to sample groundwater fauna (net hauls and pumping) in bores in two contrasting regions (Dubbo and upper Hunter Valley) of eastern Australia. Repeated sets of seasonal samples from the upper Hunter Valley bores were used to test whether once-off sampling was sufficient for compliance purposes. 3. All taxa collected by the net method were also captured in pump samples. In addition, pumping yielded more taxa, higher total abundances, and higher numbers of the two most common taxa (syncarids and copepods) than the net. Ten net hauls in the upper Hunter Valley bores collected, on average, 64% of the taxa and 44% of total abundance. When combined with the first 100 L from pumping, cumulative totals rose to 92.5% and 74.5% respectively. Similar trends occurred in bores near Dubbo, indicating that net hauls alone under-sampled groundwater faunal communities. Multivariate analyses revealed substantial differences in community composition as each incremental subsample was added. 4. Temporal changes in community composition in the Hunter Valley aquifer were marked yet inconsistent across the bores. Initial once-off sampling collected 30–87% of the total taxa from each bore and new taxa were still being collected after four sampling periods in over half the bores. This shows that more than one sampling occasion is needed for comprehensive assessments of groundwater biodiversity. 5. Successful compliance monitoring of groundwater fauna requires cost-effective sampling that will not overlook potentially vulnerable taxa or miss ecologically relevant changes in community composition. Currently, a lack of suitable bores seems to be the main constraint on accurate assessment of groundwater invertebrate community composition in these two areas of eastern Australia.

Short-range endemism is common in groundwater fauna (stygofauna), placing many species at risk from anthropogenic impacts such as water abstraction and pollution. Few of the alluvial aquifers in eastern Australia have been sampled for stygofauna. Fauna from two aquifers in Queensland and two in New South Wales was sampled to improve ecological knowledge of stygofauna and the potential threats posed to it by development. Our surveys found stygofauna in all four aquifers, with most taxa collected from bores with low electrical conductivity (<1500 μS cm⁻¹). Taxon richness decreased with distance below the water table. The most taxon-rich bores in each region occurred where the water table depth was <10 m, were associated with the alluvium of tributaries of large regulated river systems, and were near phreatophytic trees. It is possible that tree roots constitute a habitat and source of organic matter in alluvial aquifers as they do in cave streams. It is important to document the biodiversity of particular regions and aquifers so that species can be conserved in the face of increasing groundwater use. For effective resource management, future research should strive to understand the tolerances and ecological requirements of groundwater communities and the ecosystem services they provide.

Environmental flow releases have been advocated as a useful rehabilitation strategy for improving river condition but assessments of their success have typically focused on surface water quality and biota. In this study, we investigated the impacts of an environmental flow release on water temperature, conductivity, dissolved oxygen, and nitrate concentrations in surface and subsurface (hyporheic) water at upwelling an downwelling zones in three sites along the Hunter, River, New South Wales, Australia. We hypothesised that the flow pulse would 'flush' the sediments with oxygenated water, stimulating hyporheic microbial activity and nitrification, enhancing nitrate concentrations over time. Surface and subsurface samples were collected before, 7 days after, and 49 days after an environmental flow release of 5000 Ml for a period of 3 days. no lasting effects on dissolved oxygen or conductivity were evident at most sites although dissolved oxygen declined over time at the downwelling site at Bowmans Crossing. At the downwelling zones at all sites, hyporheic nitrate concentrations declined initially following the release, but then rose or levelled off by Day 49. This initial drop in concentration was attributed to flushing of nitrate from the sediments. At two sites, nitrate concentrations had increased by Day 49 in the upwelling zones while at the third site, it fell significantly, associated with very low dissolved oxygen and likely reductive loss of nitrate. Electrical conductivity data indicate that potential inputs of agriculturally enriched groundwater may contribute to the nitrogen dynamics of the Hunter River. This study highlights the spatial heterogeneity that occurs in the hyporheic zone within and among sites of a regulated river, and emphasises the need for multiple-site surveys and an understanding of groundwater dynamics to assess physicochemical responses of the hyporheic zine to environmental flow releases.

Recent surveys of groundwater invertebrates (stygofauna) worldwide are yielding rich troves of biodiversity, with significant implications for invertebrate systematists and phylogeneticists as well as ecologists and groundwater managers. What is the ecological significance of this high biodiversity of invertebrates in some aquifers? How might it influence groundwater ecosystem services such as water purification or bioremediation? In terrestrial ecosystems, biodiversity is typically positively correlated with rates of ecosystem functions beneficial to humans (e.g. crop pollination). However, the links between biodiversity, ecosystem function, and ecosystem services in groundwater are unknown. In some aquifers, feeding, movement and excretion by diverse assemblages of stygofauna potentially enhance groundwater ecosystem services such as water purification, bioremediation and water infiltration. Further, as specific taxa apparently play 'keystone' roles in facilitating ecosystem services, declines in abundance or even their extinction have serious repercussions. One way to assess the functional significance of biodiversity is to identify ecosystem service providers', characterise their functional relationships, determine how service provision is affected by community structure and environmental variables, and measure the spatio-temporal scales over which these operate. Examples from Australian and New Zealand alluvial aquifers reveal knowledge gaps in understanding the functional importance of most stygofauna, hampering effective protection of currently undervalued groundwater ecosystem services.

Ecological constraints in subsurface environments relate directly to groundwater flow, hydraulic conductivitiy, interstitial biogeochemistry, pore size, and hydrological linkages to adjacent aquifers and surface ecosystems. Groundwater ecology has evolved from a science describing the unique subterranean biota to its current form emphasising multidisciplinary studies that integrate hydrogeology and ecology. This multidisciplinary approach seeks to elucidate the function of groundwater ecosystems and their roles in maintaining subterranean and surface water quality. In aquifer-surface water ecotones, geochemical gradients and microbial biofilms mediate transformations of water chemistry. Subsurface fauna (stygofauna) graze biofilms, alter interstitial pore size through their movement, and physically transport material through the groundwater environment. Further, changes in their populations provide signals of declining water quality. Better integrating groundwater ecology, biogeochemistry, and hydrogeology will significantly advance our understanding of subterranean ecosystems, especially in terms of bioremediation of contaminated groundwaters, maintenance or improvement of surface water quality in groundwater-dependent ecosystems, and improved protection of groundwater habitats during the extraction of natural resources. Overall, this will lead to a better understanding of the implications of groundwater hydrology and aquifer geology to distributions of subsurface fauna and microbiota, ecological processes such as carbon cycling, and sustainable groundwater management