Groundwater in sufficient amounts and of suitable quality is essential for potable water supplies, crop irrigation and healthy habitats for plant and animal biocenoses. The groundwater resource is currently under severe pressure from land use and pollution and there is evidence of dramatic changes in aquifer resources in Europe and elsewhere, despite numerous policy measures on sustainable use and protection of groundwater. Little is known about how such changes affect groundwater dependent ecosystems (GDEs), which include various aquatic and terrestrial ecosystems above ground and inside the aquifer. Future management must take this uncertainty into account. This paper focuses on multiple aspects of groundwater science, policy and sustainable management. Examples of current management methods and practices are presented for selected aquifers in Europe and an assessment is made of the effectiveness of existing policies such as the European Water Framework Directive and the Habitat Directive in practice and of how groundwaters and GDEs are managed in various conditions. The paper highlights a number of issues that should be considered in an integrated and holistic approach to future management of groundwater and its dependent ecosystems.