Recent research in microbial ecology has focused on how aquatic bacterial communities are assembled. Only a few of these studies follow a “Gleasonian” approach where the roles of single bacterial populations are in focus. In this thesis, novel molecular tools were used to describe the distribution and evolutionary relationships of microbes in productive aquatic environments. Many new phylogenetic groups of bacteria were identified, likely representing bacterial populations restricted to productive freshwaters. I also addressed the dynamics and functional role of individual bacterial populations in eutrophic lakes and brackish environments with a focus on either biogeochemically significant or potentially pathogenic representatives. Flavobacteria blooms were observed, on occasions characterized by high heterotrophic production. In addition to high temporal dynamics microbial community composition and function differed on the spatial scale, as exemplified by free-living and Cyanobacteria-associated habitats. At the community scale, microbial processes, such as biomass production and substrate uptake could be predicted from the presence and absence of individual bacterial populations. I also studied the niches of potentially pathogenic Vibrio populations in various coastal waters. Using a novel culture-independent method, a V. cholerae population was detected along the entire Swedish coastline. Results from an environmental survey and a laboratory mesocosm experiment reveal that phytoplankton-derived dissolved organic matter enhance the growth of V. cholerae and other Vibrio spp. and hence create a largely overlooked niche for these heterotrophic bacteria. This thesis and future work on the role of individual bacterial populations will facilitate predictions of biogeochemical cycles and the distribution of bacteria in the context of global climate change and local eutrophication.