Abstract Seasonal and spatial variations in bacterial abundance, biomass and potential heterotrophic activity in a recently flooded reservoir were measured for two consecutive years, in conjunction with phytoplankton biomass (chlorophyll-a concentration) and activity (primary production). The mean value of primary production remained constant between the two study years, while those of the chlorophyll-a concentrations, bacterial abundance, bacterial biomass and bacterial heterotrophic activity decreased. The observed trends in the bacterial variables were linked to changes in the relative importance of allochthonous dissolved organic matter, in addition to selective grazing activity on bacterioplankton. Multivariate regression analyses identified bacterial abundance (29%) and temperature (17%) as dominant correlates of the bacterial potential heterotrophic activity. We concluded that, in a new reservoir, organic matter, other than that from phytoplankton, might be of great importance for bacterioplankton metabolism. Furthermore, grazing activity on bacteria by metazoa in a new reservoir represents, on occasion, an important trophic link between the top consumer and otherwise unavailable dissolved organic carbon sources. Finally, even if little energy is transferred to larger consumers, the microbial route is still important in re-mineralizing organic matter in Sep Reservoir.