When compared to surface ecosystems, groundwater sampling has unique constraints, including limited access to ecosystems through wells. In order to monitor groundwater, a detailed understanding of groundwater biota and what biological sampling of wells truly reflects, is paramount. This study aims to address this uncertainty, comparing the composition of biota in groundwater wells prior to and after purging, with samples collected prior to purging reflecting a potentially artificial environment and samples collected after purging representing the surrounding aquifer. This study uses DNA community profiling (metabarcoding) of 16S rDNA and 18S rDNA, combined with traditional stygofauna sampling methods, to characterise groundwater biota from four catchments within eastern Australia. Aquifer waters were dominated by Archaea and bacteria (e.g. Nitrosopumilales) that are often associated with nitrification processes, and contained a greater proportion of bacteria (e.g. Anaerolineales) associated with fermenting processes compared to well waters. In contrast, unpurged wells contained greater proportions of pathogenic bacteria and bacteria often associated with denitrification processes. In terms of eukaryotes, the abundances of copepods, syncarids and oligochaetes and total abundances of stygofauna were greater in wells than aquifers. These findings highlight the need to consider sampling requirements when completing groundwater ecology surveys.

The notion of ecosystem health has been widely adopted in environmental policy, particularly in the management of river systems. Despite this, even a notional understanding of ecosystem health and its assessment in connected aquifer ecosystems remains elusive. In this article, we propose a definition and provide a tiered framework for the assessment of ecosystem health in groundwater. From the literature we identify general attributes of a healthy groundwater ecosystem and from these develop primary (Tier 1) indicators of health. Where Tier 1 benchmarks are exceeded or more detailed assessment is required, we discuss a range of indicators (Tier 2) that may together generate a multimetric index of groundwater health. Our case study using samples from an alluvial aquifer in north-western New South Wales, Australia, demonstrates the utility of both tiers of the framework, and the ability of the approach to separate disturbed and undisturbed sites. The process of multimetric development is simple and our Tier 2 benchmarks determined from limited data. Nevertheless, our framework will be applicable and readily adaptable to site-specific contexts.

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Changes in surface land use may threaten groundwater quality and ecosystem integrity, particularly in shallow aquifers where links between groundwater and surface activities are most intimate. In this study we examine the response of groundwater ecosystem to agricultural land uses in the shallow alluvial aquifer of the Gwydir River valley, New South Wales, Australia. We compared groundwater quality and microbial and stygofauna assemblages among sites under irrigated cropping, non-irrigated cropping and grazing land uses. Stygofauna abundance and richness was greatest at irrigated sites, with the composition of the assemblage suggestive of disturbance. Microbial assemblages and water quality also varied with land use. Our study demonstrates significant differences in the composition of groundwater ecosystems in areas with different surface land use, and highlights the utility of groundwater biota for biomonitoring, particularly in agricultural landscapes.