The distributions of total CO2 (CT) and total alkalinity (AT) were determined in the Baltic Sea in summer 2008 and winter 2009, respectively. The cruises covered all major basins between the Kattegat, the north of the Gulf of Bothnia and the east of the Gulf of Finland. A CT-salinity diagram indicated that the surface water CT was mainly controlled by AT. Except for the Gulf of Riga, AT decreased with decreasing salinity and resulted in a strong CT gradient in the surface water between the Kattegat to the northern regions of the Baltic Sea. Whereas the biologically induced modulations of the AT-controlled CT distribution were relatively small in the surface layer, the effect of the organic matter decomposition on the CT levels in the below-halocline water was large. The CT fraction generated by mineralization (minCT) in the deeper water layers was determined from the difference between the measured CT and the preformed CT. The preformed CT was estimated on the basis of the CO2 partial pressure and the AT which the considered deep water mass had during its last contact with the atmosphere. The minCT accumulation was largest in the deep basins of the central Baltic Sea where maximum values of up to 450 µmol kg− 1 were found in the bottom water of the Gotland Sea. This was attributed to long-lasting stagnation periods and to an intense organic matter input. Considerably lower minCT (factors 4–5) were obtained for the Gulf of Bothnia due to both a more frequent deep water renewal and a reduced organic matter flux.