• A physically-based semi-distributed hydrological model and a 1D stream water temperature model forced by climate change scenarios is presented here to analyze the effects of stream flow and water temperature changes on fish habitat in the Athabasca River catchment. • Streamflow decreases in most of the catchment will reduce flow velocities and water depths causing current Athabasca Rainbow Trout habitat to be suboptimal. • Increases in water temperature will result in habitat contraction concentrating Athabasca Rainbow Trout in the upper headwaters of the catchment. • Athabasca Rainbow Trout habitat can potentially be reduced as the frequency of occurrence of life threatening and lethal water temperatures tend to increase, particularly in summer. Changes to natural flow and air temperature in the context of climate change can have impacts on physiology, distribution and survival of fish. Of particular interest is the Athabasca River basin, a highly biologically productive basin that includes one of the largest boreal freshwater inland river deltas in the world and serves as habitat for many fish species. Earlier melt events, higher winter and spring flows and lower summer flows are expected as a consequence of climate change in this basin. Here, we model changes in river flow and water temperature under changing climate scenarios through the integration of a physically-based semi-distributed hydrological model and a 1D stream water temperature model forced by climate change scenarios. The modeled changes in streamflow and water temperature are used to predict changes in habitat suitability for the Athabasca Rainbow Trout (ART) ( Oncorhynchus mykiss ), a unique ecotype of trout considered as a ‘species at risk’. The results indicate that future flow decreases in most of the basin can lead to reduced flow velocities and water depths making current ART habitat suboptimal. Also, warming low-land habitats and increasing water temperatures will increase metabolic rates and stress fish forcing them to migrate upstream to cooler waters confining their habitat range.