Freshwater ecosystems are facing mounting challenges. The widespread introduction of nonnative species, for example, has resulted in the loss of native species and the substantial reconfiguration of diversity patterns across regions. Documenting such impacts remains critical for informing national-level biosecurity policies. Here, we explore changes in biogeographic patterns in freshwater fish diversity in response to the spread of nonnative species, teasing apart the geographic (watersheds) and taxonomic (species) drivers of patterns at the global scale. We leveraged global databases of fish species occurrence to estimate the unique contributions of local watershed and species (native and nonnative origin) contributions to beta-diversity for biogeographic domains. We report significant changes in freshwater fish beta-diversity in response to nonnative species, with the largest impacts in the Afrotropics, Nearctic and Palearctic domains. Even though, nonnatives decreased contribution of watersheds to beta-diversity in all domains, particularly in watersheds with known impacts. Watersheds identified as the most important for promoting beta-diversity were not evenly within across domains, were influenced by geographical isolation, and their unique composition were composed by many endemic and threatened species. Species contributions to enhancing beta-diversity were higher for natives, and threatened species. Relatedly, the species from the most important watersheds had wide ecological tolerances, were in general natives, endemics and/or with IUCN threat status. Our findings underscore the widespread consequences of nonnative species for shaping biogeographic patterns of freshwater fishes in the Anthropocene.