We examined impacts of future climate scenarios on flow regimes and how predicted changes might affect river ecosystems. We examined two case studies: Cle Elum River, Washington, and Chattahoochee-Apalachicola River Basin, Georgia and Florida. These rivers had available downscaled global circulation model (GCM) data and allowed us to analyse the effects of future climate scenarios on rivers with (1) different hydrographs, (2) high future water demands, and (3) a river-floodplain system. We compared observed flow regimes to those predicted under future climate scenarios to describe the extent and type of changes predicted to occur. Daily stream flow under future climate scenarios was created by either statistically downscaling GCMs (Cle Elum) or creating a regression model between climatological parameters predicted from GCMs and stream flow (Chattahoochee-Apalachicola). Flow regimes were examined for changes from current conditions with respect to ecologically relevant features including the magnitude and timing of minimum and maximum flows. The Cle Elum's hydrograph under future climate scenarios showed a dramatic shift in the timing of peak flows and lower low flow of a longer duration. These changes could mean higher summer water temperatures, lower summer dissolved oxygen, and reduced survival of larval fishes. The Chattahoochee-Apalachicola basin is heavily impacted by dams and water withdrawals for human consumption; therefore, we made comparisons between pre-large dam conditions, current conditions, current conditions with future demand, and future climate scenarios with future demand to separate climate change effects and other anthropogenic impacts. Dam construction, future climate, and future demand decreased the flow variability of the river. In addition, minimum flows were lower under future climate scenarios. These changes could decrease the connectivity of the channel and the floodplain, decrease habitat availability, and potentially lower the ability of the river to assimilate wastewater treatment plant effluent. Our study illustrates the types of changes that river ecosystems might experience under future climates.