Declining streamflow induces collapse and replacement of native fish in the American Southwest

Water scarcity is a global threat to freshwater biodiversity, but connecting variation in streamflow to viability of imperiled faunas remains a challenge. Here we combined time-series modeling techniques on long-term ecohydrological data to quantify flow–ecology relationships on native and non-native riverine fish in the American Southwest, and simulate likely fish trajectories and “quasi-extinction” risks in the near future. Streamflow has been declining conspicuously over the past 30 years in the Colorado and Rio Grande river basins, and year-to-year variation in streamflow influences the covariation between native and non-native fish abundance. Risks of decline are high (>50%) for nearly three-quarters of the modeled native species, and current trends in streamflow increase quasi-extinction risk for natives (+8.5%) but reduce this risk for non-natives (–5.9%). Hydrological changes need to be mitigated if we are to slow down the rapid replacement of native biodiversity with non-native species in American Southwest rivers.