The qualitative and quantitative characteristics of the heterotrophic microbial communities (bacteria, flagellates, and ciliates) in the thin water-sediment layer in the Kara Sea are analyzed. The bacterial abundance correlated with the concentration of organic matter, whereas their size depended on the abundance of heterotrophic flagellates. The number of species of heterotrophic flagellates increased with the increase in the bacterial number. A positive relationship between the bacterial abundance and the ration of heterotrophic flagellates was observed at the offshore stations, probably due to the grazing pressure. The density of the ciliates on the soft silty and sandy-silty sediments was extremely low. The share of upstream filter feeding ciliate species increased with the increase in the abundance of the flagellates, probably due to the shift to less selective feeding strategies at higher values of the food concentrations. The classification of the heterotrophic microbial communities in the surface sediment layer has revealed two distinct types of the communities. The river communities are rich in species and are characterized by the high abundance of microorganisms. They are gradually replaced by marine communities at the salinity of 9%.