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.

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.

Active exchanges of water and dissolved material between the stream and groundwater in many porous sand- and gravel-bed rivers create a dynamic ecotone called the hyporheic zone. Because it lies between two heavily exploited freshwater resources - rivers and groundwater - the hyporheic zone is vulnerable to impacts coming to it through both of these habitats. This review focuses on the direct and indirect effects of human activity on ecosystem functions of the hyporheic zone. River regulation, mining, agriculture, urban, and industrial activities all have the potential to impair interstitial bacterial and invertebrate biota and disrupt the hydrological connections between the hyporheic zone and stream, groundwater, riparian, and floodplain ecosystems. Until recently, our scientific ignorance of hyporheic processes has perhaps excused the inclusion of this ecotone in river management policy. However, this no longer is the case as we become increasingly aware of the central role that the hyporheic zone plays in the maintenance of water quality and as a habitat and refuge for fauna. To fully understand the impacts of human activity on the hyporheic zone, river managers need to work with scientists to conduct long-term studies over large stretches of river. River rehabilitation and protection strategies need to prevent the degradation of linkages between the hyporheic zone and surrounding habitats while ensuring that it remains isolated from toxicants. Strategies that prevent anthropogenic restriction of exchanges may include the periodic release of environmental flows to flush silt and re-oxygenate sediments, maintenance of riparian buffers, effective land use practices, and suitable groundwater and surface water extraction policies.

Previous studies on recovery in hyporheic communities have found that communities rapidly return to predisturbance levels. However, most of these studies have concentrated on small floods or ones with shortreturn periods. I studied the impact of a large 1 in 6 year flood on the hyporheic community at 2 sites in the Hunter River, a large coastal river in New South Wales with a mean daily flow of 15 m³ s⁻¹. The flood peaked at 1270 m³ s⁻¹ and afterwards invertebrate densities at the 2 sites were 83 and 67% less than they were before. Recovery to pre-flood densities was slow but was aided by increases in the oligochaete and cyclopoid populations. At Site 1, there was a boom in oligochaete and cyclopoid numbers 61 d after the flood, but the communities resumed their pre-flood densities by Day 139. Recovery at Site 2 took 139 d. Most groundwater taxa (stygobites) living in the hyporheic zone did not recover from the disturbance when compared to non-stygobites. Apart from Microturbellaria and the harpacticoid 'Parastenocaris' sp., numbers of all stygobite taxa continued to decline after the flood, becoming absent after 61 d. The poor recovery of stygobites is probably due to their adaptations for survival in the relatively stable groundwater environment. This study shows that hyporheic communities are sensitive to large bed-moving floods and supports the hypothesis that ecotonal species with a strong affinity to one ecosystem can be poor at recovering from disturbances that occur in an adjacent ecosystem.

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.

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.