The European eel (Anquilla anquilla) has been declining throughout its area of distribution, is addressed in several pieces of legislation, and is the target of extensive restoration efforts. Therefore, investigating and conserving natural eel habitats is urgently needed. Large, near-natural rivers have become rare in Europe but the Balkans host some of the extant examples. However, several Balkan rivers–among them the transboundary river Vjosa/Aoos of Albania and Greece–are under threat from planned hydropower constructions. This study synthesizes European eel catch data from four institutions and the results of a recent electrofishing survey. Population density and structure as well as habitat choice were studied at different spatial scales. We calculated densities for each meso-habitat (0–1303 ind./ha) and extrapolated these values across three different hydromorphological channel sections (meandering: 70 ind./ha, braided: 131 ind./ha, constrained: 334 ind./ha), resulting in an overall mean density of 168 ind./ha. Proposed hydropower plants would cut off about 80% of the catchment currently accessible and impact river sections downstream of the dams by disturbing hydrological dynamics. By linking study results to relevant legislation and literature we provide evidence-based data for water management decisions. We call for the Vjosa/Aoos to be protected in order to secure its outstanding conservation value.