Implementation of the European Union (EU) Water Framework Directive (WFD 2000) and its planned supplement ‘Directive on the Protection of Groundwater against Pollution’ (EU GWD [European Union Groundwater Directive] 2003) demands an initial characterization of all groundwater bodies by national and regional authorities. The main criteria considered in the Directives to define the groundwater (GW) status are quality (chemical) and quantity, but there is the obvious omission of ecological perspective in these. A directive for a comprehensive policy dealing with GW protection at the level of the EU is a prerequisite for human welfare. Additionally, recognition of GW-dependent ecosystems (GDEs) in the EU is equally important for their sustainable management. GW management and policy should recognize the ecological functions of GW and their interactions with GDEs. As they can stretch across national and regional boundaries, political recognition of their importance and the necessity for ecological consistency of management plans have to be emphasized. During the last three decades, a number of researchers have focused their attention on the dynamics and functioning of GW ecosystems and this work could serve as a basis for identifying impacts of changes in key attributes of GDEs. Detailed aspects of GW ecosystems have been comprehensively dealt with (Gibert et al. 1994; Wilkens et al. 2000; Griebler et al. 2001; Danielopol et al. 2003). Changes in key attributes of GW ecosystems have had consequences for the environment in the EU and USA (Klijn & Witte 1999; Winter 1999; Sophocleous 2002; Winter et al. 2003).