Marine microbial communities are highly dynamic, respond to environmental drivers and change on spatial and temporal scales. In the Baltic Sea, recent surveys show that the salinity gradient structures bacterioplankton community composition. Yet, these surveys were conducted during summer when environmental conditions were relatively stable. The spring bloom is initiated by near-zero temperatures, depletes inorganic nutrients and is the major source of organic matter in the system. In this study, bacterioplankton dynamics, phytoplankton and environmental parameters were monitored during the transition of the spring bloom on transects across the Baltic Proper, from Finland to Germany. Using next generation amplicon sequencing of the 16S rRNA gene, we studied the bacterial community composition during the general transition of the plankton community from new to regenerated production. We show that on short temporal scales, the microbial community composition varies across large spatial scales. Gammaproteobacteria and Betaproteobacteria were highly abundant in the open Baltic Proper, and were strongly correlated to phosphate availability during early stages of the spring bloom. During the mature bloom stage, the bacterioplankton communities was highly similar along the entire transect, dominated by Bacteroidetes, Actinobacteria and Alphaproteobacteria. Compared to other surveys we found that salinity is not solely driving the Baltic Sea bacterioplankton community composition during spring bloom conditions. Thus, changes in nutrient availability, timing and transition of the bloom can act as selective forces, structuring microbial communities.