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Kandalaksha Bay is a peculiar estuarine system located at the Arctic Circle within the White Sea semi-enclosed basin (Russia). This sub-extreme marine environment combines features of temperate and Arctic seas. Its unusual hydrodynamic is due to seasonal high runoff of freshwater (caused by inputs from rivers and abundant precipitations), and tidal currents generating intense mixing mainly of surface waters. In order to get a survey of the bacterial community of this zone, seawater was sampled, at various distances from the shore and depths, in areas selected in relation to the tidal current pattern. Bacterial assemblages were characterised by 454-pyrosequencing to obtain detailed information on their diversity and structure. The phylum Proteobacteria was the most predominant in all samples (abundance ranged from 67% to 96%), being the class γ-Proteobacteria its main fraction. Cyanobacteria was the second most abundant phylum (11–15%) in surface samples collected offshore in the main tidal stream, while it was rather scarce in the coastal samples and very low at the maximum depth. Unexpectedly, no presence of Synechococcus was detected; in addition, the diffused occurrence of Prochlorococcus , generally very low or absent in polar waters, could be considered another effect of global change. Bacteroidetes showed abundance ≥5% in surface and shallow waters (15 m). At the genus level, biodiversity clearly decreased in the offshore samples, in particular at the highest depth, were high prevalence of Halomonas was recorded (>65%). The Redundancy Analysis revealed that water temperature and salinity represented the environmental factors determining the bacterial community structure. Moreover, the nMDS analysis evidenced high similarity only among samples taken in surface layers and involved in the water mixing by tidal currents, being the deepest sample (−70 m) the most dissimilar. • First NGS survey of bacterial communities of Kandalaksha Bay Arctic estuarine system • Proteobacteria dominated in all samples with γ-Proteobacteria as its main fraction. • Diffused occurrence of Prochlorococcus (low or absent in polar waters) was recorded. • Community driving factors were water temperature and salinity (RDA analysis). • Water mixing by currents influenced distribution and composition of the communities. [ABSTRACT FROM AUTHOR]