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.