The regulation of aquatic carbon cycles by temperature is a significant uncertainty in our understanding of how watersheds will respond to climate change. Aquatic ecosystems transport substantial quantities of carbon to the atmosphere and ocean, yet we have limited understanding of how temperature modifies aquatic ecosystem metabolic processes and contributions to carbon cycles at watershed to global scales. We propose that geomorphology controls the distribution and quality of organic material that forms the metabolic base of aquatic ecosystems, thereby controlling the response of aquatic ecosystem metabolism to temperature across landscapes. Across 23 streams and four years during summer baseflow, we estimated variation in the temperature sensitivity of ecosystem respiration (R) among streams draining watersheds with different geomorphic characteristics across a boreal river basin. We found that geomorphic features imposed strong controls on temperature sensitivity; R in streams draining flat watersheds was up to six times more temperature sensitive than streams draining steeper watersheds. Further, our results show that this association between watershed geomorphology and temperature sensitivity of R was linked to the carbon quality of substrates that changed systematically across the geomorphic gradient. This suggests that geomorphology will control how carbon is transported, stored, and incorporated into river food webs as the climate warms.