We explored the whole-lake accumulation of CO2 during winter ice cover and in the hypolimnion during summer stratification, in 15 temperate and boreal lakes, and how these processes vary with lake trophic state and morphometry. We further estimated an annual CO2 budget for each lake that incorporates the fluxes resulting from winter ice-cover and summer hypolimnetic CO2 accumulation to assess their relative importance. The volumetric rates of CO2 accumulation during the winter ice cover ranged from 4.1 to 42.1 mg C m−3 d−1, and from 9.3 to 54.5 mg C m−3 d−1 in the summer hypolimnion, and both varied mainly as a function of water temperature. The total CO2 accumulation at the end of winter/summer was most strongly related to lake mean depth and was significantly greater under ice than in the hypolimnion. This greater CO2 accumulation resulted in relatively high and unvarying spring outflux, averaging 404 mg C m−2 d−1 (C.V. 27%). Significant hypolimnetic CO2 accumulation also resulted in relatively high fluxes (average 228 mg C m−2 d−1) during autumnal mixing, which were more variable (C.V. 43%) than spring fluxes. Average fluxes were lowest and most variable in summer (198 mg C m−2 d−1, C.V. 46%). The net annual CO2 flux ranged from 14 to 68 g C m−2 y−1, and was positively related to DOC concentration. The winter ice-cover CO2 accumulation accounted from 3 to 80% (average 17%) of the annual CO2 flux, whereas summer hypolimnetic accumulation accounted for a smaller but still significant proportion (from 1.4 to 46%). These winter and summer hypolimnetic CO2 accumulations are released to the atmosphere through short but intense emission bursts that are rarely captured in regular lake sampling schemes, yet they have the potential to profoundly influence the annual lake CO2 budgets in northern landscapes.