Freshwater pro-and eukaryotic microorganisms and viruses are interconnected by trophic interactions that form complex food webs. The labile dissolved organic carbon in the pelagic zone is consumed by bacteria which in turn are grazed by unicellular protistan predators. This results in a recycling of growth-limiting nutrients for the phytoplankton and in the transfer of particulate organic carbon and nutrients to higher trophic levels. The success of microbial populations in aquatic environments is dependent on their ability to outgrow the mortality inflicted by protistan grazing and viral lysis while competing for limited resources. Various microbial phenotypic adaptations are therefore aimed at reducing loss rates by predation. Heterotrophic protists, in turn, selectively target particular bacterial morphotypes or species. Bacterioplankton assemblages are thus composed of different genotypic populations that are particularly well adapted to cope with either top-down (predation defense) or bottom-up (resource competition) factors. Since pelagic microbial food webs are set against a background of spatial heterogeneity, the microscale patchiness of resource distribution and mortality allows for a coexistence of bacterial species with different growth strategies. The high overall stability of aquatic prokaryotic assemblages at the community level thus probably results from the variable temporal dynamics of numerous individual bacterial populations.