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.

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.

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.