Substrate supply and protist grazing are two of the most important forces that determine the composition and properties of bacterial assemblages. General ecological theory predicts that the relative importance of these factors is changing with the environmental productivity. In the present study, the interplay between bottom-up and top-down control was studied in a productivity gradient simulated in one-stage chemostats containing natural assemblages of freshwater bacteria and heterotrophic nanoflagellates. Bacterial assemblages in the chemostats differed strongly with respect to their morphological, physiological and compositional properties in the presence versus the absence of predators. However, theses differences were modified by the productivity gradient. Whereas in predator-free chemostats the mean abundance and biomass of bacteria increased proportionally with increasing substrate supply, in treatments that included flagellates bacterial production was largely channelled into predator biomass. The bacterial morphological diversity increased along the productivity gradient with increasing substrate input but even more so with predators. Proportional to the increasing substrate supply, predation shifted the remaining bacteria towards morphologically inedible forms. Predation also caused shifts in bacterial substrate-utilization profiles, and in bacterial community composition, as analysed by terminal restriction fragment length polymorphism of PCR-amplified 16S-rRNA genes. Without predators, bacterial richness increased along the productivity gradient whereas with predators bacterial richness was higher at intermediate substrate levels. In accordance with ecological theory, these results demonstrated that predators influence all of the major characteristics of bacterial assemblages but the magnitude of this effect is modulated by the productivity of the system.