Natural fires annually decimate up to 1% of the forested area in the boreal region of Québec, and represent a major structuring force in the region, creating a mosaic of watersheds characterized by large variations in vegetation structure and composition. Here, we investigate the possible connections between this fire-induced watershed heterogeneity and lake metabolism and CO2 dynamics. Plankton respiration, and water–air CO2 fluxes were measured in the epilimnia of 50 lakes, selected to lie within distinct watershed types in terms of postfire terrestrial succession in the boreal region of Northern Québec. Plankton respiration varied widely among lakes (from 21 to 211 μg C L−1 day−1), was negatively related to lake area, and positively related to dissolved organic carbon (DOC). All lakes were supersaturated in CO2 and the resulting carbon (C) flux to the atmosphere (150 to over 3000 mg C m2 day−1) was negatively related to lake area and positively to DOC concentration. CO2 fluxes were positively related to integrated water column respiration, suggesting a biological component in this flux. Both respiration and CO2 fluxes were strongly negatively related to years after the last fire in the basin, such that lakes in recently burnt basins had significantly higher C emissions, even after the influence of lake size was removed. No significant differences were found in nutrients, chlorophyll, and DOC between lakes in different basin types, suggesting that the fire-induced watershed features influence other, more subtle aspects, such as the quality of the organic C reaching lakes. The fire-induced enhancement of lake organic C mineralization and C emissions represents a long-term impact that increases the overall C loss from the landscape as the result of fire, but which has never been included in current regional C budgets and future projections. The need to account for this additional fire-induced C loss becomes critical in the face of predictions of increasing incidence of fire in the circumboreal landscape.