The aim of this study was to investigate the importance of winter season for the production of carbon dioxide (CO2) and methane (CH4) in humic and clear-water boreal aquatic systems. The study was conducted in 16 experimental ponds in northern Sweden during the winter of 2013. Half of the ponds had a higher concentration of dissolved organic carbon (DOC). CO2, CH4, DOC and dissolved inorganic carbon (DIC) were measured repeatedly under the ice from January to April. The results show that CO2 was accumulated continually during winter. No difference in winter accumulation were found between humic and clear ponds. CH4 was rarely accumulated in neither humic nor clear ponds, and was not an important part of the gas flux at spring ice melt. At ice melt, the flux from humic ponds accounted for 1.6 g C m-2 and 1.7 g C m-2 from clear ponds, which was equivalent for 15.6% respective 100% of the annual gas emissions. On a whole-year basis humic ponds acted as a source of 10.3 g C m-2, while clear ponds acted as a sink of 14.7 g C m-2. 76 mg m-2 d-1 DOC was consumed in humic and 59 mg m-2 d-1 DOC in clear ponds while the DIC accumulation was 125 mg m-2 d-1 in humic and 118 mg m-2 d-1 in clear ponds. This study stresses the importance of ice-covered boreal aquatic systems as a significant parts of the global carbon cycling.