Dramatic and unprecedented changes in the composition of ecological communities may be a feature of the Anthropocene, challenging the integrity and function of ecosystems and their management. Ecological communities in flowing freshwaters may be particularly vulnerable to these changes because of their exposure and vulnerability to a wide range of anthropogenic impacts. Here we apply a new statistical method for detecting such changes to > 2100 time series of freshwater fish communities spanning the years 1972 to 2018 and distributed across the globe. We find coincident rapid and unprecedented compositional changes emerged in 16% (95% CI: 14.5%-17.6%) of the fish communities surveyed over the last 50 years, with similar rates of emergence in Europe, North America and Australasia. Novel community states emerged with probability 0.021 (95% CI: 0.016 – 0.028) across all year-to-year transitions across all communities in the database, and had probability 0.33 of persisting over multiple years. Not surprisingly, the emergence of novel communities tended to be positively associated with metrics of anthropogenic impact, and increases in the abundance of exotic species. Our findings demonstrate that novel ecological communities in flowing freshwaters are a feature of the Anthropocene.