Many canyon‐bound rivers have been dammed and downstream flow and water temperatures modified. Climate change is expected to cause lower storage in reservoirs and warmer release temperatures, which may further alter downstream flow and thermal regimes. To anticipate potential future changes, we first need to understand the dominant heat transfer mechanisms in canyon‐bound river systems. Towards this end, we adapt a dynamic process‐based river routing and temperature model to account for complex shading and radiation characteristics found in canyon‐bound rivers. We apply the model to a 362 km segment of the Colorado River in Grand Canyon National Park, USA to simulate temperature over an 18‐year period. Extensive temperature and flow datasets from within the canyon were used to assess model performance. At the most downstream gaging location, root mean square errors of hourly flow routing and temperature predictions were 11.5 m³/s and 0.93 °C, respectively. We found that heat fluxes controlling temperatures were highly variable over space and time, primarily due to shortwave radiation dynamics and hydropeaking flow conditions. Additionally, the large differences between air and water temperature during summer periods resulted in high sensible and latent heat fluxes. Sensitivity analyses indicate that reservoir release temperatures are most influential above the RM88 gage (141 kilometers below Glen Canyon Dam), while a combination of discharge, shortwave radiation, and air temperature become more important farther downstream. This study illustrates the importance of understanding the spatial and temporal variability of topographic shading when predicting water temperatures in canyon‐bound rivers.