The population dynamics of heterotrophic nanoflagellates (HNF) were analyzed in pre-alpine Lake Constance over three consecutive years. A recurrent seasonal pattern led to the identification of five seasonal phases: winter, spring, clear-water, summer and autumn. HNF biomass was lowest in winter and highest m late spring several weeks after the phytoplankton spring bloom. The average biomass of HNF was 5–12% of bacterial biomass and 13–34% of ciliate biomass respectively. The largest HNF cells were recorded during the spring phase, whereas the average cell size was reduced to one-third during the subsequent clear-water phase. The pronounced differences in the mean cell size were attributed mainly to varying grazing impact on HNF Throughout most of the year, HNF production was balanced by grazing of microzooplankton, namely ciliates, within the microbial loop. During the dear-water phase, however, the grazing impact was mainly due to rotifers and daphnids. Changing grazing impact was primarily responsible for the observed 2-fold interannual difference m the mean biomass of HNF Overall, top-down control by grazing was more important in governing the population dynamics of HNF than bottom-up control by bacterial food supply.