Estuarine bacteria are key modifiers of allochthonous matter entering the sea, and thereby control major biogeochemical processes such as nutrient cycling and organic matter transformation. In a highly dynamic estuarine environment, bacterial growth and activity are regulated by multiple factors including the availability of organic carbon, inorganic nutrient concentrations, salinity and temperature. The variability of estuarine bacterial communities in relation to environmental factors and dissolved organic matter (DOM) quantity and quality was studied in three Baltic Sea estuaries with different catchment characteristics, flow and mixing regimes. The work was conducted during six consecutive seasons over 2 years. Bacterial activity, biomass and cytometric cell population characteristics were studied against an suite of environmental parameters and DOM quality and quantity (Salinity, DOC, DON and DIN concentration, SUVA254, UV Slope275–295, Fluoresecence peaks A and T, and Apparent mean molecular weight). Environmental variables and DOM quality varied significantly between rivers, indicating influence of catchment characteristics. Bacterial biomass varied significantly between the sampling seasons, and bacterial production also varied between the rivers, indicating an influence of DOM quality on bacterial activity. Based on cytometric grouping into low- and high- nucleic acid bacterial populations (LNA and HNA, respectively) salinity-dependent and salinity-independent clusters of bacterial variables were identified. The results suggest that the LNA clusters were not directly dependent on salinity, but possibly linked to humic substance degradation, whereas the HNA clusters were linked to salinity-correlated environmental variables reflecting DOM quality. Mixed-effects regression modeling of bacterial biomass turnover time suggests DOM fluorescence properties to be useful proxies of bioavailability. Our study shows that growth and community dynamics of estuarine bacteria may be partially regulated by quality of riverine DOM, and cytometric sub-populations of estuarine bacteria have differing regulative factors.