Groundwater contributes to the maintenance of the functioning of ecosystems, through aspects related to hydrodynamics and chemical composition. Groundwater-dependent ecosystems (GDE) also offer a wide spectrum of ecosystem services to populations; therefore, their identification and mapping, which is the focus of the present paper, is of high value to environmental policies; for example, WFD envisages protecting both water bodies and GDE. An ecosystem dependence index was applied to proceed with this task in the Azores archipelago, being estimated by adding the values of three partial variables (spring density; wetlands/lakes; river baseflow) over a 10 by 10 m2 grid; with this methodology avoiding pitfalls due to lack of data. The results enabled the identification and mapping of five GDE, in Flores and São Miguel islands, supported by only three of the 28 groundwater bodies delimited in the Azores RBD. Those groundwater bodies are considered to have a good status according to the WFD requirements; thus, GDE, regardless of their typology, are not at risk of deterioration as a result of the interaction with groundwater. Nevertheless, other studies have shown that some GDE are in conflicting ecological areas and require specific management and protection measures, coupling land use and water resource planning.