Eutrophication results from nutrient overload in aquatic ecosystems and affects primary productivity patterns, which impacts the living conditions of aquatic organisms. The rivers in the catchment area of the Baltic Sea are greatly affected by eutrophication, but impacts on fish functional diversity are poorly understood. This study, therefore, evaluates the effects of freshwater eutrophication on fish functional diversity in the rivers of the Baltic Sea catchment area. Total phosphorus is used as the eutrophication indicator. Functional richness, evenness, and divergence values were calculated using comprehensive fish trait and occurrence databases. Functional evenness was found to be negatively related to eutrophication. Functional divergence demonstrated a positive relation but responded to lesser extents than functional evenness. Functional richness showed no or a negative response, depending on whether environmental covariates were considered. As a comparison, species richness revealed a negative relationship and was the most responsive to increasing eutrophication of all measures evaluated. Hence, this study demonstrates the varying nature of responses of multiple diversity indices and comprehensively describes the response of fish communities to increasing eutrophication in the area. The results show that functional redundancy helps to reduce adverse effects of species losses on functional diversity, which provides an important starting point for impact assessment. The findings illustrate that actions to limit nutrient discharge to freshwater are needed to maintain sustainable riverine ecosystems.