Cyanobacterial blooms have a strong impact on the food web structure, interactions and ecosystem functioning. The aim of this study was to describe the seasonal changes in composition and abundance of heterotrophic nanoflagellates, ciliates, rotifers, and crustaceans in relation to algae and nutrients in a shallow eutrophic lake (north-eastern Poland) dominated by cyanobacteria and exposed to the strong impact of cormorants. Our results showed that algae accounted for a small part of the total phytoplankton abundance (9–40%) and biomass (10–21%) and were dominated by diatoms and cryptophytes. All of the studied groups of planktonic organisms were quite rich in species (95 algal, 79 ciliate, 44 rotifer and 25 crustacean species) and relatively abundant. Copepods formed a substantial part (45–83%) of the total zooplankton biomass during all seasons. Relatively low algal to zooplankton biomass ratio (0.8–1.1) suggests that during spring, summer, and winter algae were not sufficient food resources for metazooplankton, which supplemented its diet with protists (heterotrophic nanoflagellates and ciliates). In a shallow lake dominated by cyanobacteria, winter (ice-covered period) may be a more favourable period for the growth of some groups of algae, ciliates and rotifers than other seasons due to decreasing abundance of cyanobacteria.