How carbon cycles are regulated by environmental temperature remains a substantial uncertainty in our understanding of how watersheds will respond to ongoing climate change. Aquatic ecosystems are important components of carbon flux to the atmosphere and ocean, yet we have limited understanding of how temperature modifies ecosystem metabolic processes and, therefore, aquatic contributions to carbon cycles at watershed to global scales. We propose that geomorphology controls the landscape-scale distribution and quality of organic material that forms the metabolic base of aquatic ecosystems and, therefore, how aquatic ecosystem metabolism responds to changes in temperature. Across 23 streams and four years in a boreal river basin, we estimated how temperature sensitivity of ecosystem respiration (ER) varied among streams draining watersheds with different geomorphic characteristics. We found that geomorphic conditions imposed strong ultimate controls on temperature sensitivity; ER in streams draining flat watersheds was up to six times more sensitive to temperature than streams draining steeper watersheds. Further, we show that the link between watershed geomorphology and temperature sensitivity of ER was related to the quality of carbon substrates that changes systematically across the gradient in geomorphic conditions. These results suggest that geomorphology will ultimately control how carbon is transported, stored, and incorporated into river food webs as climate warms.