A community hosted by an ecosystem composed of species sharing the same characteristics i.e. species showing the same response to the environment and/or species with the same impact on their environment, can be define as a community with high functional redundancy. Such community is supposed to be less vulnerable to species loss and the ecosystem functioning is also supposed to be less impacted than when communities are composed of species with different functional characteristics. In this work, we first described the fish communities of lakes, rivers and estuaries of France, Spain and Portugal using species richness and functional diversity. Functional diversity was a measure of the extent of complementary among species considering five characteristics previously define by different sources (literature, available database): fish size, vertical position in the water body, spawning habitat, trophic group, and swimming mode. For the three aquatic systems, the number of species and functional diversity was generally higher in northern and western France than in the Mediterranean areas; this geographical pattern was explained by historical events (last glacial period). Higher functional diversity shown in estuaries compare to lakes and rivers was explained by the importance of the connectivity between adjacent environments. Analysing correlations between functional redundancy and species richness, results suggest that higher taxonomic richness in freshwater ecosystems is likely to increase the stability and resilience of fish assemblages after environmental disturbance because of higher species redundancy whereas it is not the case in estuaries. Studying the impact of species loss according different scenarios, we also demonstrated that, in rivers and estuaries, rare species support singular ecological functions not shared by dominant species. Our results suggest also that functional diversity of fish assemblages in rivers can be more affected by environmental disturbances than in lakes and estuaries. Finally, using functional redundancy and taxonomic vulnerability, we proposed a composite index of functional vulnerability, minimised for highly redundant assemblages composed of species with low extinction risk. Fish communities of estuarine ecosystems appear less vulnerable to species loss in comparison with assemblages of lakes and rivers. Although these latter systems obtained comparable scores, the functional vulnerability was not influenced by the same component. Fish assemblages in lakes are often redundant but composed of a large part of vulnerable species, whereas river assemblages are in general poorly redundant but composed of species with low intrinsic vulnerability. This new score is proposed to be used in conservation perspective to define management priorities.