We studied the seasonal dynamics of phytoplankton, bacterioplankton, heterotrophic nanoflagellates, ciliates, and metazoan plankton in the highly eutrophic polymictic Lake Kastoria (Greece), which has a history of toxic cyanobacterial blooms. An acute increase in the flushing rate of the lake during spring inhibited cyanobacterial biomass accumulation. During this transient oligotrophic period, which was characterized by abundant lake snow particles, the plankton food web was an inverted biomass pyramid (low autotrophic biomass and high heterotrophic biomass). Prokaryotes played a key role in these changes (cyanobacteria during periods of autotrophy and bacteria during periods of heterotrophy). In summer and autumn, toxic cyanobacterial blooms developed, and the microbial loop was weak. The microbial loop was weak because the heterotrophic nanoflagellates and nanociliates decreased to undetectable densities during the summer, when larger bacterivores (rotifers and small cladocera) were abundant. Toxic blooms may have a dual effect on heterotrophic nanoplankton: negative during the first bloom and postbloom period and positive during a following toxic bloom. Different species (Cylindrospermopsis raciborskii, Aphanizomenon spp., and Microcystis aeruginosa) and succession phases of toxic blooms may differentially affect the microbial food web structure.In pelagic systems, phytoplankton and bacterioplankton constitute the complementary functional components that primarily produce new particulate matter by autotrophy and heterotrophy. Their carbon pool represents the base of grazing food chains and the microbial loop. Thus, the relative dominance of each functional component has significant implications for food web structure and the function and bio- AcknowledgmentsWe would like to thank the two anonymous reviewers and Associate Editor R. Bachmann for their constructive criticisms and suggestions. We are grateful to U. Sommer for his critical comments and suggestions on drafts of this manuscript and to U. Christaki for her helpful comments. We thank L. Economou for linguistic suggestions and C. M. Cook for the critical reading of sections of the manuscript concerning cyanotoxins. This work was partially funded by the Municipality of Kastoria, Research Committee, Aristotle University of Thessaloniki, project 7468. We thank all participating members of this project.

Primary productivity, pico‐, nano‐, microplankton and key environmental factors were studied in a eutrophic coastal area of the Aegean Sea during the winter – spring period. Primary productivity reached high values and showed similar trends of change to those of nanophytoplankton abundance. Nano‐ and microplankton cell densities showed high variability while picoplankton abundance was kept relatively stable. Diatoms dominated nanophytoplankton for most of the winter – spring period while a shift to dinoflagellates was initiated with the development of thermal stratification in late spring. Ciliates and heterotrophic dinoflagellates reached high densities in contrast to heterotrophic nanoflagellates. Our results emphasize the close relation between grazer densities and bacteria, cyanobacteria and nanoplanktic algal changes in this eutrophic coastal area of the Mediterranean.