Abstract Understanding long‐term changes in fish diversity and community assembly rules is crucial for freshwater conservation. Growing evidence indicates that studying functional and phylogenetic diversity beyond purely taxonomic considerations can provide different but complementary information on community assembly. Here, the taxonomic, functional, and phylogenetic β‐diversity of fish communities, as well as the community assembly mechanisms, were explored in five impounded lakes of the China's South‐to‐North Water Diversion Project (SNWDP) from the 1980s to the 2010s. We found that (1) there was an obvious trend of species homogenization in the five impounded lakes, but the long‐term transformations of different dimensional β‐diversity were divergent; (2) water quality and land use variables have greater impacts on multidimensional β‐diversity; and (3) community assembly process in taxonomic and functional dimensions were dominated by random process in both periods, while shifting from limiting similarity to habitat filtering in the phylogenetic dimension. These results highlight that functional and phylogenetic diversity are important additional ecological indices for assessing the patterns of fish diversity in lakes.
