Dramatic environmental changes and species invasions are increasingly threatening the diverse fish fauna of the Yellow River, China. This study examines temporal changes in the alpha and beta components of fish taxonomic, functional and phylogenetic diversity in relation to anthropogenic environmental changes over the past 50 years. We hypothesized that temporal trends in multifaceted components of diversity would be highly congruent, but that the relative importance of anthropogenic disturbances would differ in shaping spatial patterns of fish diversity. We found that all three components of alpha diversity increased over time but at different rates (19.1%, 21.3% and 15.3% for taxonomic, functional and phylogenetic diversity, respectively). Fish faunas of the Yellow River have also become homogenized over time, but this was much greater for functional and phylogenetic components of beta diversity than for taxonomic diversity (change in beta diversity = - 0.11, - 0.24 and - 0.02, respectively). Temporal changes in alpha and beta diversity were strongly related to invasion of non-native fish species and changes in temperature, sediment load, reservoir capacity and aquaculture area. Our results underscore the ongoing need for threat mitigation (particularly relating to dams and aquaculture) to conserve the unique biodiversity of one of the world's largest rivers.