In this paper, we assess the extent to which the export of terrestrially fixed carbon to aquatic systems and the aquatic metabolism of this carbon affect the overall accumulation of organic carbon in a boreal catchment. We estimated the contribution of stocks and processes in aquatic environments to the carbon balance of a boreal catchment in northern Sweden. We used published data concerning the net ecosystem exchange (NEE) of CO2 in terrestrial environments, and calculations of loss of terrestrial carbon to surface water and the turnover of terrestrial carbon in aquatic systems. The NEE of terrestrial environments was estimated to be 139 g C/m2 of catchment area per year. The export of terrestrially fixed carbon to aquatic systems was 8.6 g C/m2/yr, resulting in a net accumulation of organic carbon in terrestrial systems of 131 g C/m2/yr. Almost 45% of the terrestrial export was mineralized in streams and lakes and evaded as CO2, while most of the remaining (approximately 55%) terrestrial export was transported to the sea as organic carbon or as dissolved inorganic carbon emanating from soil respiration. The sedimentation of organic carbon and input of organic carbon via aquatic primary production were insignificant when compared to the mineralization and river transport of terrestrial organic carbon. Aquatic fluxes were small compared to the terrestrial NEE, which we consider to be largely a consequence of the studied catchment being subject to intensive forestry resulting in a large annual accumulation of carbon in growing tree biomass.