Numerous studies have estimated carbon exchanges at the land–atmosphere interface, more recently also including estimates at the freshwater–atmosphere interface. Less attention has been paid to lateral carbon fluxes, in particular to the fate of terrestrial carbon during transport from soils via surface waters to the sea. Using extensive datasets on soil, lake and river mouth chemistry of the boreal/hemiboreal region we determined organic carbon (OC) stocks of the O horizon from catchment soils, annual OC transports through more than 700 lakes (OClakeflux) and the total annual OC transport at Sweden's 53 river mouths (OCseaflux). We show here that a minimum of 0.03–0.87% yr−1 of the OC soil stocks need to be exported to lakes in order to sustain the annual OClakeflux. Across Sweden we estimated a total OClakeflux of ~2.9 Mtonne yr−1, which corresponds to ~10% of Sweden's total terrestrial net ecosystem production, and it is over 50% higher than the total OCseaflux. The OC loss during transport to the sea follows a simple exponential decay with an OC half-life of ~12 years. Water colour, a proxy often used for dissolved humic matter, is similarly lost exponentially but about twice as fast as OC. Thus, we found a selective loss of the coloured portion of soil-derived OC during its transport through inland waters, prior to being discharged into the sea. The selective loss is water residence time dependent, resulting in that the faster the water flows through the landscape the less OC and colour is lost. We conclude that increases in runoff will result in less efficient losses of OC, and particularly of colour, if the time for OC transformations in the landscape shortens. Consequently, OC reaching the sea is likely to become more coloured, and less processed, which can have far-reaching effects on biogeochemical cycles.