Salinity, other physico-chemical parameters and anthropogenic pollution are the main factors affecting bacterial communities in estuaries. We estimated the impact of these parameters on the distribution of bacterial communities in the Adour estuary (France), a moderately Polluted water body characterized by short residence times of particles and water and absence of a maximum turbidity zone. Eight stations were established along the salinity gradient from freshwater to marine conditions. For the 3 typical estuarine stations (water mixing zone), samples were collected at both low and high tide and at different depths according to the position of the halocline. This sampling strategy generated 35 samples with different degrees of mixing between fresh water and seawater. All the samples were characterized by their physico-chemical parameters and trace metal contents (as a contamination tracer). The structure of bacterial communities was determined by T-RFLP fingerprinting. The metal-salinity profiles suggested dilution processes and/or usual geochemical reactivity for the elements sensitive to sorption/desorption mechanisms (Cd, Mn). Metal concentrations were low, with no evidence of contaminated plumes, suggesting that metal concentrations were not influencing bacterial diversity. A well-established estuarine bacterial community was observed, comprising mostly Cyanobacteria, Planctomyces and Alphaproteobacteria. This community was different from fresh and seawater communities, and a shift in community composition was observed between 10 and 34 PSU. Although residence time in the Adour estuary is very short, the salinity and halocline in this water body are likely to be the main parameters influencing bacterial community composition.