Lakes and reservoirs typically emit CO2to the atmosphere as a result of respiration in excess of primary production. For reservoirs, this respiration is often assumed to be primarily of benthic origin, associated with drowned vegetation and soils. This study took measurements from a young hydroelectric reservoir (Eastmain-1) in boreal Canada and nearby natural lakes to compare the rates of water column respiration and hypolimnetic CO2 accumulation during a stratified period. Reservoir water column respiration rates were significantly higher than those in natural lakes, with surface means of 61.4 ± 4.6 mg C m−3 d−1in Eastmain-1 and 40.2 ± 3 mg C m−3 d−1 in lakes and profundal means of 58.1 ± 11 mg C m−3 d−1in Eastmain-1 and 17.6 ± 7.5 mg C m−3 d−1 in lakes. Reservoir hypolimnetic CO2 accumulation rates were also higher than those in natural lakes, with means of 78.8 ± 16 mg C m−3 d−1in Eastmain-1 and 19.8 ± 2.7 mg C m−3 d−1 in lakes. Our findings further indicate that the relative contribution of benthic respiration (estimated as the difference between hypolimnetic CO2 accumulation and water column respiration) toward total net CO2production during stratified periods was similar in both aquatic systems (23% in lakes, 27% in Eastmain-1). By identifying the major role of the water column in the reservoir's CO2 production, this study calls for a significant paradigm shift away from the common assumption that reservoir CO2 emissions are predominantly the result of decaying vegetation in the benthic environment.