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The objective of this study was to quantitatively assess the relative importance of terrigenous dissolved organic material (TDOC) as a carbon source for secondary producers (e.g. bacteria) and as a structuring factor for the pelagic food web in the Gulf of Bothnia, northern Baltic Sea. The 3 study sites, situated in Bothnian Bay (BB), the re Estuary (E) and the Bothnian Sea (BS), had markedly different freshwater loads and water-residence times. In Bothnian Bay, bacterial biomass and production were higher than expected from the levels of phytoplankton biomass and productivity there, suggesting an uncoupling of bacterial productivity from phytoplankton production. Phytoplankton size structure and size-fractionated production were, however, relatively similar among areas. A simplified carbon budget model suggested that bacterioplankton dominated organic carbon consumption in all of the food webs studied, but was most marked in BB. The model showed that the available autochthonous primary production could not alone support the heterotrophic carbon demand in BB. The most likely explanation of this discrepancy was that the total annual input of terrigenous dissolved organic carbon was bioavailable, resulting in a budget closer to balance with the heterotrophic carbon demand. BB, receiving 38% of the carbon input from land, was consequently a net heterotrophic ecosystem. A sensitivity analysis showed that the bacterial carbon demand, and growth efficiency in particular, had the greatest influence on the resulting budget. TDOC was the dominant carbon source in E, but the losses of carbon through advection to offshore areas and sedimentation was high. The evidence of net heterotrophy in E was therefore weaker than in BB. In BS the input of TDOC was less important, and the carbon used for secondary production originated mainly from autochthonous primary production. Our results suggest that the supply of TDOC is of great importance for the abundance of plankton and as a structuring factor for the aquatic food webs in the Gulf of Bothnia.