As demand for consumptive use of groundwater escalates, the need for careful management becomes more pressing. Water reforms in Australia require explicit recognition of environmental needs in water resource plans, but subsurface groundwater dependent ecosystems (SGDEs) are rarely provided for. The ecological values of these sequestered ecosystems are not well documented and are readily overlooked. We review the biodiversity, ecological processes and ecosystem services of Australian SGDEs and highlight the ecological relevance of their connectivity with other ecosystems. A lack of attention to SGDEs in groundwater plans risks inadequate provision for environmental water requirements with probable impacts on ecological values, water quality and ecosystem goods and services in SGDEs and connected ecosystems. We suggest an ecohydrogeological approach to understanding the implications of anthropogenic disturbance on SGDEs based on their connectivity to other ecosystems and aquifer permeability. As well as a template for comparative research on the biogeochemistry and ecology of SGDEs in Australia and overseas, this conceptual tool has potential application in conservation planning, water resource assessment and environmental impact assessment.