The quest to understand species’ distribution patterns and delineate their limits has led to the establishment of the world’s ecoregions, large units of land containing a distinct assemblage of species, both for terrestrial and marine ecosystems. However, freshwaters constitute their own special case within terrestrial ecosystems, and have only recently been divided into freshwater ecoregions, primarily based on watershed limits. Freshwater ecoregions used by the European Water Frame Directive (WFD), which guides freshwater management policies in the European Union, have been criticized for not adequately representing freshwater fish biogeography. This study compares the geographic agreement between WFD ecoregions and freshwater fish distribution at the European scale. Using IUCN Red List distribution maps, we determined the composition of freshwater fish communities in major European basins. Then, we calculated a similarity matrix in order to cluster freshwater basins with more related fish assemblages. We compare our findings with WFD ecoregions and global ecoregions from the Freshwater Ecoregions of the World (FEOW) database. Our results reveal that WFD ecoregions do not sufficiently capture freshwater fish assemblage differences across Europe. Mediterranean basins exhibit high freshwater fish endemism and greater species variation, whereas central European basins harbor more similar fauna. Overall, our results align more with those of FEOW. To enhance the relevance of freshwater ecoregions in Europe for management and conservation, we propose several measures to ensure a comprehensive study involving all stakeholders in the process of defining these ecoregions accurately.