Climate change is projected to have an enormous effect on water resources in the western US, with cascading effects on river-dependent organisms. Recent studies show that increasing drought will lead to reduced water in many rivers in the southwestern US. For example, streamflow in the warm season has declined over the last century in the western US and is projected to continue decreasing over the next 100 years. In arid and semi-arid regions of the western US, it is likely that some perennial streams will shift to intermittent flow in response to climate-driven changes in runoff and evapotranspiration. We addressed the following two questions: (1) how will small stream low flows be affected by warmer conditions in the Upper Colorado River Basin (UCRB) and (2) how will riparian vegetation respond? To address these questions we (1) modeled stream low flow metrics on ungaged streams in the UCRB and (2) sampled riparian vegetation along a hydrologic gradient (perennial to intermittent) to develop statistical relationships between flow parameters and biotic responses. We found the majority of perennial and weakly intermittent streams that are threatened under warmer conditions to be small, high elevation streams. Further, with our field vegetation data we are able to suggest how riparian plant communities will shift in the future and how managers can draw from these results for restoration planning in the context of climate change.