In parts of the Baltic Sea, the phytoplankton spring bloom communities, commonly dominated by diatoms, are shifting towards the co-occurrence of diatoms and dinoflagellates. Although phytoplankton are known to shape the composition and function of associated bacterioplankton communities, the potential bacterial responses to such a decrease of diatoms are unknown. Here we explored the changes in bacterial communities and heterotrophic production during the spring bloom in four consecutive years across several subbasins of the Baltic Sea and related them to changes in environmental variables and in phytoplankton community structure. The taxonomic structure of bacterioplankton assemblages was partially explained by salinity, temperature but also linked to shifts in phytoplankton communities. Higher carbon biomass of the diatoms Achnanthes taeniata, Skeletonema marinoi, Thalassiosira levanderiand Chaetoceros spp. was associated with a highly diverse bacterial community dominated by copiotrophic bacteria (Flavobacteriia, Gammaproteobacteria and Betaproteobacteria) and higher bacterial production rates, whereas during dinoflagellate dominance bacterial production was low and communities were dominated by Alphaproteobacteria, mainly by the oligotrophic SAR11. Our results suggest that increases in dinoflagellate abundance upon diatoms during spring bloom will largely affect the structuring and functioning of the associated bacterial communities, which might have drastic consequences for the pelagic remineralization of organic matter.