Groundwater dependent ecosystems (GDEs) include many terrestrial and aquatic systems with high biodiversity and important ecosystem services. The need for protection of these systems has recently received increasing recognition in many regions, including the European Union (EU), as pressures on groundwater are increasing due to increased consumption in agriculture and intensive land use. A key issue is to provide legislative frameworks that safeguard the ecosystem services these systems provide. This paper reviews European legislation and present methods for theoretical frameworks, and hydrological and ecological observations of GDEs. Insights into the current state of research are provided and gaps in scientific knowledge identified. Different restoration and protection measures, such as buffer zones, are presented and evaluated. Recommendations are given for the future protection of GDEs. Future research should focus on nationally important GDE sites to establish conceptual models describing the individual and interactive impacts of multiple stressors on the hydrological and ecological functioning of GDEs. Proactive management is required to protect GDEs from contamination, for example by using extended buffer zones and careful land use planning in the groundwater capture zone.

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