Microbial communities of the Arctic Ocean are poorly described in comparison to aquatic environments of other regions regarding their patterns of distribution and change. The present work aims to investigate free-living bacterial communities (size fraction 0.22–1.5 μm) of different Arctic seas regions, from the river discharge area to the continental slope. Illumina MiSeq metabarcoding analysis using V3–V4 region of 16S rRNA gene was employed to study the microbial diversity of 11 Arctic seawater samples, collected from the surface and near-bottom layers in the Kara and Laptev Seas in August–September 2018. Additionally, we determined environmental parameters, bacterial abundance, biomass, and respiratory activity. Redundancy analysis, Spearman’s rank correlation, and multiple linear regression analysis were used to reveal environmental factors that modulate the bacterial community structure. The differences in the free-living bacterial community composition were associated with environmental characteristics of water layers (salinity and temperature) rather than with geographical area. Although the communities from all examined sites were dominated by Gammaproteobacteria and Alphaproteobacteria followed by Flavobacteriia and Actinobacteria, they showed distinct variations in the distribution at all taxonomical levels. No archaeal taxa were observed. The distribution patterns of the quantitative parameters of total bacterial community were not associated with defined environmental characteristics.