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.