We calculated the carbon loss (mineralization plus sedimentation) and net CO2 escape to the atmosphere for 79 536 lakes and total running water in 21 major Scandinavian catchments (size range 437–48 263 km2). Between 30% and 80% of the total organic carbon that entered the freshwater ecosystems was lost in lakes. Mineralization in lakes and subsequent CO2 emission to the atmosphere was by far the most important carbon loss process. The withdrawal capacity of lakes on the catchment scale was closely correlated to the mean residence time of surface water in the catchment, and to some extent to the annual mean temperature represented by latitude. This result implies that variation of the hydrology can be a more important determinant of CO2 emission from lakes than temperature fluctuations. Mineralization of terrestrially derived organic carbon in lakes is an important regulator of organic carbon export to the sea and may affect the net exchange of CO2 between the atmosphere and the boreal landscape.