Hypertrophic aquatic ecosystems are biologically important because they represent an environment where homeostatic mechanisms are strongly reduced and extreme oscillations occur in physical and chemical parameters as well as in the growth of many planktonic organisms. Hypertrophic lakes may represent not only the ultimate state of eutrophication, but also systems where abundance and production of picoplanktonic organisms (0.2–2 μm in diameter) may theoretically be greatest. In this review we examined the microbial ecology literature for studies on hypertrophic lakes and assessed the significance of heterotrophic bacteria (BACT) and autotrophic picoplankton (APP). Our main conclusions are as follows: (a) The relative contribution of APP to total phytoplankton biomass is strongly reduced in hypertrophic systems. (b) The absolute abundance and biomass of APP are highly variable among these systems; depending mainly on differences in light quality and quantity, the existence of nitrogen limitation and presence of pollutants. (c) The abundance of BACT does not increase as rapidly as algal biomass with increasing trophy. (d) A clear dichotomy exists between lakes dominated by Microcystis where bacterial biomass and production are relatively low, and Planktothrix‐dominated lakes where bacterial biomass and production are high. (e) Bacterial production per unit biomass tends to increase from oligotrophic to hypertrophic systems supporting the previous hypothesis that bacteria do not play a lesser role in lake metabolism at the upper end of the trophic scale. In general, however, our knowledge of the microbial ecology of hypertrophic systems has advanced very little since the 1980s, largely because most studies of these systems have focused on their remediation.