In the past, the phrase ‘environmental allocations of water’ has most often been taken to mean allocation of water to rivers. However, it is now accepted that groundwater-dependent ecosystems are an important feature of Australian landscapes and require an allocation of water to maintain their persistence in the landscape. However, moving from this theoretical realisation to the provision and implementation of a field-based management regime is extremely difficult. The following four fundamental questions are identified as being central to the effective management of groundwater-dependent ecosystems (GDEs): (1) How do we identify GDEs in the field; put another way, which species or species assemblages or habitats are reliant on a supply of groundwater for their persistence in the landscape; (2) what groundwater regime is required to ensure the persistence of a GDE; (3) how can managers of natural resources (principally water and habitats), with limited time, money and other resources, successfully manage GDEs; and (4) what measures of ecosystem function can be monitored to ensure that management is effective? This paper explicitly addresses these questions and provides a step-by-step theoretical and practical framework for providing answers. In particular, this paper provides an introduction to some of the relevant literature and from this, presents a synthesis, presented in the form of a functional methodology for managing groundwater dependent ecosystems.

Groundwater is a vital ecosystem of the global water cycle, hosting unique biodiversity and providing essential services to societies. Despite being the largest unfrozen freshwater resource, in a period of depletion by extraction and pollution, groundwater environments have been repeatedly overlooked in global biodiversity conservation agendas. Disregarding the importance of groundwater as an ecosystem ignores its critical role in preserving surface biomes. To foster timely global conservation of groundwater, we propose elevating the concept of keystone species into the realm of ecosystems, claiming groundwater as a keystone ecosystem that influences the integrity of many dependent ecosystems. Our global analysis shows that over half of land surface areas (52.6%) has a medium‐to‐high interaction with groundwater, reaching up to 74.9% when deserts and high mountains are excluded. We postulate that the intrinsic transboundary features of groundwater are critical for shifting perspectives towards more holistic approaches in aquatic ecology and beyond. Furthermore, we propose eight key themes to develop a science‐policy integrated groundwater conservation agenda. Given ecosystems above and below the ground intersect at many levels, considering groundwater as an essential component of planetary health is pivotal to reduce biodiversity loss and buffer against climate change.