Managing the world’s freshwater supply to meet societal and environmental needs in a changing climate is one of the biggest challenges for the 21st century. Dams provide water security, however, the allocation of dwindling water supply among reservoirs could exacerbate or ameliorate the effects of climate change on aquatic communities. Here, we show that the relative sensitivity of river thermal regimes to direct impacts of climate change and societal decisions concerning water storage vary substantially throughout a river basin. In the absence of interspecific interactions, future Colorado River temperatures would appear to benefit both endemic and nonnative fish species. However, endemic species are already declining or extirpated in locations where their ranges overlap with warmwater nonnatives and changes in water storage may lead to warming in some of the coolest portions of the river basin, facilitating further nonnative expansion. Integrating environmental considerations into ongoing water storage negotiations may lead to better resource outcomes than mitigating nonnative species impacts after the fact.