Microbial communities living in stratified lakes are known to be early indicators of ecosystem disturbances. Based on information available up to date it was hypothesized that structures of heterotrophic bacteria and phytoplankton assemblages in the eutrophic lake are shaped by different, yet interrelated physicochemical parameters and both groups significantly influence each other. To verify this hypothesis, the species distribution of these groups along the environmental gradients in a eutrophic lake (Lake Góreckie, NW Poland) was investigated. During the study 198 phytoplankton and 26 bacteria taxa were detected in 84 samples. The analysis of their temporal and spatial distribution revealed that phytoplankton and bacteria respond to ecological gradients in a roughly independent manner. Temperature, NH4+ and total phosphorus turned out to be the most important environmental gradients for the phytoplankton, while of concentrations oxidized nitrogen forms (NO3-, NO2-) were more relevant for heterotrophic bacteria. The results obtained in this study allowed us to identify cluster of culturable bacteria connected with high concentrations of chlorophyll a (and thus with the presence of phytoplankton). The group of phytoplankton-associated bacteria includes strains identified as Bacillus megaterium, B. simplex, Paenibacillus amylolyticus, Enterobacter cancerogenus and all the detected members of genus Exiguobacterium. These results are the next step towards an understanding of the microbial food web functioning in eutrophic lakes; an understanding which is crucial in the context of the protection and management of these ecosystems.