These data were compiled for a manuscript in which 1) we develop a water temperature model for the major river segments and tributaries of the Colorado River basin, including the Colorado, Green, Yampa, White, and San Juan rivers; 2) we link modeled water temperature to fish population data to predict the probability native and nonnative species will be common in the future in a warming climate; and 3) assess the degree to which dams create thermal discontinuity in summer in river segments across the western US. Per goal #1, we developed a water temperature model using data spanning 1985-2015 that predicts water temperature every 1 mile (1.6-km) in rivers both now and in the future due to the potential influence of climate change and human decisions on water storage in reservoirs that affect temperature. Data inputs to the water temperature model include air temperature, discharge, water temperature, and solar radiation. Base model data are included in the 'WaterT Model-Base Data' and 'WaterT Model-Base Summary' data tables, future air temperature predictions are included in the 'WaterT Model-CMIP AirT' data table, and reservoir elevations are included in the 'WaterT Model-Reservoir Storage' data table. These data were used to generate water temperature predictions used in Figures 1-4 in the associated manuscript. Per goal #2, we calculated the number of Thermally Suitable Days (TSDs) in each river segment for Colorado pikeminnow (Ptychocheilus lucius), razorback sucker (Xyrauchen texanus), humpback chub (Gila cypha), smallmouth bass (Micropterus dolomieu), red shiner (Cyprinella lutrensis), and channel catfish (Ictalurus punctatus) using species-specific thermal minimums, maximums, and optimums for growth ('TSD-TemperatureTolerance' data table) and mean monthly predicted water temperatures by reach from the base model ('TSD-WaterT' data table). We compare summarized decadal-scale endangered humpback chub population estimates from 1990-2018 for multiple populations relative to TSDs in the 'Humpback Chub PopEst' data table. We include endangered Colorado Pikeminnow population estimates from 2001-2018 relative to smallmouth bass removals in the 'Colorado Pikeminnow PopEst' data table. These are data presented in Figure 3 in the associated manuscript. Circle size is weighted to TSDs per data in the data table. Per goal #3, we take the difference between mean July air temperature and water temperature released from dams and compare this 'discontinuity' to the depth from which water was withdrawn from the reservoir in the 'Therm Discontinuity Data' data table. Data summarized for these 3 goals were obtained from the U.S. Geological Survey, National Water Information System, Glen Canyon Dam Monitoring and Research Center (USGS), U.S. Fish and Wildlife Service San Juan River Basin Recovery Implementation Program, NOAA National Climatic Data Center, National Solar Radiation Database, the USBR Hydromet Data System, and from published literature.