We analysed N2- and carbon (C) fixation in individual cells of Baltic Sea cyanobacteria by combining stable isotope incubations with secondary ion mass spectrometry (SIMS). Specific growth rates based on N2- and C-fixation were higher for cells of Dolichospermum spp. than for Aphanizomenon sp. and Nodularia spumigena. The cyanobacterial biomass, however, was dominated by Aphanizomenon sp., which contributed most to total N2-fixation in surface waters of the Northern Baltic Proper. N2-fixation by Pseudanabaena sp. and colonial picocyanobacteria was not detectable. N2-fixation by Aphanizomenon sp., Dolichospermum spp. and N. spumigena populations summed up to total N2-fixation, thus these genera appeared as sole diazotrophs within the Baltic Sea's euphotic zone, while their mean contribution to total C-fixation was 21%. Intriguingly, cell-specific N2-fixation was eightfold higher at a coastal station compared to an offshore station, revealing coastal zones as habitats with substantial N2-fixation. At the coastal station, the cell-specific C- to N2-fixation ratio was below the cellular C:N ratio, i.e. N2 was assimilated in excess to C-fixation, whereas the C- to N2-fixation ratio exceeded the C:N ratio in offshore sampled diazotrophs. Our findings highlight SIMS as a powerful tool not only for qualitative but also for quantitative N2-fixation assays in aquatic environments.