||Aim Human activities and the consequent extirpations of native species and introductions of non-native species have been modifying the composition of species assemblages throughout the world. These anthropogenic impacts have modified the richness of assemblages as well as the biological dissimilarity among them. However, while changes in taxonomic dissimilarity (i.e. accounting for species composition) have been assessed intensively during the last decade there are still few assessments of changes in functional dissimilarity (i.e. accounting for the diversity of biological traits). Here, we assess the temporal changes in both taxonomic and functional dissimilarities for freshwater fish assemblages across Europe. Location Western Palaearctic, 137 river basins. Methods The Jaccard index was used to quantify the changes in both taxonomic and functional dissimilarity. We then partitioned dissimilarity to extract its turnover component and measured the changes in the contribution of turnover to dissimilarity. Results Functional homogenization exceeded taxonomic homogenization six-fold. More importantly, we found only a moderate positive correlation between these changes. For instance, 40% of assemblages that experienced taxonomic differentiation were actually functionally homogenized. Taxonomic and functional homogenizations were stronger when the historical level of taxonomic dissimilarity among assemblages was high and when a high number of non-native species were introduced in the assemblages. Moreover, translocated species (i.e. non-native species originating from Europe) played a stronger role than exotic species (i.e. those coming from outside Europe) in this homogenization process, while extirpation did not play a significant role. Main conclusions Change in taxonomic diversity cannot be used to predict changes in functional diversity. In addition, as functional diversity has been proven to be a better indicator of ecosystem functioning and stability than taxonomic diversity, further studies are required to test the potential effects of functional homogenization at the local scale.