Significance Understanding the mechanisms by which biological communities are reorganized by environmental change is a key question facing ecologists. Using a global database of fish abundance time series spanning recent decades, together with community-level indices describing species temperature and flow affinities, we show that two important aspects of climate change (water temperature and streamflow alteration) are interacting with land-use modification to drive increases in the dominance of species that prefer warm- and slow-water habitats. Although these community reorganizations show substantial geographical variation, they can be explained by a combination of degree of environmental changes and initial community composition. These findings offer insights to improve ecological forecasting in the future to better inform and prioritize conservation actions in freshwater ecosystems.