Lakes play an important role in the cycling of organic matter in the boreal landscape, due to the frequently high extent of bacterial respiration and the efficient burial of organic carbon in sediments. Based on a mass balance approach, we calculated a carbon budget for a small humic Swedish lake in the vicinity of a potential final repository for radioactive waste in Sweden, in order to assess its potential impact on the environmental fate of radionuclides associated with organic matter. We found that the lake is a net heterotrophic ecosystem, subsidized by organic carbon inputs from the catchment and from emergent macrophyte production. The largest sink of organic carbon is respiration by aquatic bacteria and subsequent emission of carbon dioxide to the atmosphere. Although the annual burial of organic carbon in the sediment is a comparatively small sink, it results in the build-up of the largest carbon pool in the lake. Hence, lakes may simultaneously disperse and accumulate organic-associated radionuclides leaking from a final repository.