Most lakes are oversaturated with CO2 and are net CO2 sources to the atmosphere, yet their contribution to the global carbon cycle is poorly constrained. Their CO2 excess is widely attributed to in-lake oxidation of terrestrially produced dissolved organic carbon. Here we use data collected over 26 years to show that the CO2 in 20 lakes is primarily delivered directly through inflowing streams rather than being produced in situ by degradation of terrestrial carbon. This implies that high CO2 concentrations and atmospheric emissions are not necessarily symptoms of heterotrophic lake ecosystems. Instead, the annual mean CO2 concentration increased with lake productivity and was proportional to the estimated net primary productivity of the catchment. Overall, about 1.6% of net primary productivity (range 1.2–2.2%) was lost to the atmosphere. Extrapolating globally, this is equivalent to CO2 losses of ~0.9 Pg C yr−1 (range 0.7–1.3), consistent with existing estimates. These data and our catchment productivity hypothesis re-enforce the high connectivity found between lakes, their catchment and the global C cycle. They indicate that future concentrations of CO2 in lakes, and losses to the atmosphere, will be highly sensitive to altered catchment management and concomitant effects of climate change that modify catchment productivity.