Organic carbon (OC) mineralization in freshwaters is dependent on oxygen availability near the sediments, which controls whether OC inputs will be buried or respired. However, oxygen dynamics in waterbodies are changing globally due to land use and climate, and the consequences of variable oxygen conditions for OC burial are unknown. We manipulated hypolimnetic oxygen availability in a whole‐reservoir experiment and used a mass balance OC model to quantify rates of OC burial. Throughout summer stratification, we observed that OC burial rates were tightly coupled to sediment oxygen concentrations: oxic conditions promoted the mineralization of “legacy” OC that had accumulated over years of sedimentation, resulting in negative OC burial. Moreover, our study demonstrates that fluctuating oxygen conditions can switch ecosystem‐scale OC burial in a reservoir between positive and negative rates. Consequently, changing oxygen availability in freshwaters globally will likely have large implications for the role of these ecosystems as OC sinks.