In the epilimnion of Mondsee, a mesotrophic hard‐water lake in Austria, bacterial numbers were strongly but inversely correlated with the abundance of heterotrophic nanoflagellates (HNF). The mean size of pelagic heterotrophic bacteria was small (0.04–0.05 µm3) for most of the summer, with short rods and cocci dominating. During the peak of small cyanobacteria which followed a Dinobryon bloom, however, large and elongated bacteria appeared and mean bacterial cell volume increased to 0.19 µm3. This phase lasted several days, then the size structure reverted to the previous condition with small and spherical cells predominating. Bacterial numbers peaked shortly after the decline of the algal bloom, and HNF reached their highest density ∼1 week after the biomass maximum of bacteria. Diel changes of bacterial biomass, however, were of the same order of magnitude as seasonal ones. We hypothesize that small, flagellated predators, but also Dinobryon, were able to control the abundance of pelagic bacterial populations (top down) for almost the whole summer. Bacterial size, on the other hand, was significantly correlated with the abundance of phytoplankton, suggesting that bacterial cell volumes depend primarily on nutrient supply (bottom up). Consequently, the importance of both control modes to the bacterial biomass can change rapidly.