To estimate Holocene changes in organic carbon mass accumulation rates (Corg MARs) in the southeastern Swedish Baltic Sea, two sediment cores were studied in combination with biogeochemical modelling. Prior to 11 300 cal. BP, Corg MARs were extremely low, indicating low organic matter production on the catchment of the Baltic Ice Lake. Following a brief regression, the Ancylus Lake stage occurred between 11 100 and 9800 cal. BP. Corg MARs increased substantially during this period because of enhanced washing in of terrestrial organic matter, when boreal forests were initially established. The prominent marine stage, known as the Littorina transgression between 8500 and 3000 cal. BP, is marked by a minor increase in Corg MARs. Our modelling reveals a changing terrestrial organic carbon input between 100 and 1000 g/m2 per yr that accounts for 30—80% of total organic carbon in sediments of the southeastern Swedish Baltic Sea, with maximum values ( c. 20 × 103g/m2 per yr) occurring during the Bronze/Iron Age transition at about 3000 cal. BP. Corg MAR in the entire Baltic basin is estimated at 3.01 × 106 t/yr during the pre-industrial Holocene, comparable with other large inland water bodies. Regardless of the source of carbon, our data indicate that the Baltic basin is an important sedimentary reservoir for organic carbon storage and thus should be included in accounting for global terrestrial carbon cycling during the pre-industrial Holocene.