Lake CO2 emissions are an important component of the carbon balance of northern landscapes, yet the temporal dynamics of the underlying mechanisms sustaining CO2 emissions are less understood. Here, we reconstruct the major biotic and abiotic processes influencing CO2 dynamics over an annual cycle in three limnologically different lakes, using a combination of empirical measurements and process-based modeling. Our results suggest that the relative importance of each process sustaining CO2 emissions is not only variable among lakes, but also highly variable among seasons within one lake. Spring CO2 emissions were largely sustained by the release of under ice accumulation (between about 50–100%), although photo-chemical DOC mineralization and hydrologic CO2 loading were also relatively important. In summer, due to warmer temperature, pelagic and benthic metabolism were the main sources of CO2 emissions. In the fall, lake CO2 emissions were generally sustained by hydrologic CO2 inputs, while hypolimnetic CO2 accumulation and release also contributed to fall CO2 emission in the deepest lake. On an annual basis, lake CO2 emissions ranged between 21.4 g C m−2 yr−1 and 55.5 g C m−2 yr−1. Our results confirm that the major processes all contributed significantly to CO2 emissions, but their relative contributions were modulated by the seasonal patterns in climate and hydrology, and by differences in morphology and organic carbon inputs among lakes. These lake- and season-specific features need to be considered both in the upscaling of lake processes at regional scales, and in predicting lake CO2 emissions under scenarios of climate and environmental change.