In the Baltic Sea, cyanobacterial community is mainly composed of filamentous nitrogen-fixing forms, including the toxic Nodularia spumigena, and single-celled picocyanobacteria (Pcy), represented by Synechococcus spp. The main aim of the work was to test the hypothesis that the picocyanobacteria dependend on the presence of the nitrogen-fixing cyanobacteria. In addition, the contamination of blue mussels and fish with nodularin (NOD), the N. spumigena toxin, was examined. In years 2008-2011, the samples for the study were collected in the Southern Baltic Proper using FerryBox system and, occasionally, during research cruises. The analyses showed no correlation between the growth of the nitrogen-fixing cyanobacteria and Synechococcus. Compared with the previously published data, a shift in the composition of Pcy phenotypes was observed. This shift might be an indication of the proceeding changes induced by the reduced nutrient loading and/or climate change. Analyses of NOD revealed differences in the cyanotoxin concentrations between mussels of different shell size. The highest concentration of NOD was detected in the liver of round goby. However, temporarily, also the fish muscles were significantly contaminated with the toxin.