Littoral zones at the interface of the lake and the catchment are intensive sites for mineralization of organic matter, but the contribution of vegetated littoral zone to winter fluxes of carbon dioxide (CO2) and methane (CH4) from lake ecosystems into the atmosphere is poorly known. We studied littoral carbon gas fluxes and their spatial controls at five boreal lakes of varying trophic state during three consequent winters with contrasting snow conditions and flooding regimes. Lake‐wide estimates including littoral winter release and potential pelagic spring pulse of gases were calculated for three lakes. Large interannual and spatial differences in carbon gas fluxes were controlled by the interaction of climatic factors, ice and snow cover, on‐site hydrology, and apparently substrate supply from biomass production of the previous growing season. Littoral CO2 fluxes ranged from 0.9 to 7.5 mol m−2 winter−1, and the CH4 fluxes ranged from 0.04 to 0.38 mol m−2 winter−1, the latter being highest in eutrophic lakes. The vegetated littoral contributed the most (66–78%) to winter CH4 emissions from two lakes; in the smallest and most productive lake, pelagic accumulation exceeded littoral release. The large variation in littoral CO2 release could contribute to between‐winter differences of 82% in lake‐wide carbon gas emissions. The water level of the preceding summer and precipitation during early winter were found to be useful predictors for littoral carbon gas fluxes in winter. This suggests that the carbon gas exchange of a shallow boreal lake can be highly sensitive to changes in snowfall and subsequent flooding.