The impact of salinity on the composition and functional performance (biomass production, growth efficiency and growth rates) of bacterial communities was investigated using batch cultures growing on dissolved organic carbon from a river draining into the Northern Baltic Sea. The cultures were adjusted to riverine or estuarine salinity levels and inoculated with bacteria from these two environments. Bacterial growth efficiencies differed in response to salinity and the origin of the inoculum. When salinity was adjusted to correspond to the salinity at the site where the inoculum was retrieved, growth efficiency was relatively high (11.5±2.6%). However, when bacteria were confronted with a shift in salinity, growth efficiency was lower (7.5±2.0%) and more of the utilized carbon was respired. In contrast, growth rates were higher when bacteria were exposed to a change in salinity. The composition of the bacterial communities developing in the batch cultures differed, as shown by 16S rDNA DGGE, depending on the origin of the inoculum and salinity. Reverse and direct DNA–DNA hybridization revealed salinity optima in the growth of specific bacterial strains as well as broader phylogenetic groups. Strains belonging to the α- and β-Proteobacteria, Actinobacteria and γ-Proteobacteria other than the genus Pseudomonas showed higher relative abundance under freshwater conditions, whereas strains of the genus Pseudomonas and the Cytophaga–Flavobacterium–Bacteroides group were favored by estuarine conditions. Generally, our results demonstrate functional changes associated with changes in community composition. We suggest that even moderate changes in salinity affect bacterial community composition, which subsequently leads to altered growth characteristics.