The biogeochemical processes participating in the transformation of the particulate matter into sediment along the Yenisei River-St. Anna Trough (Kara Sea) meridional profile were studied using hydrochemical, geochemical, microbiological, radioisotope, and isotope methods. The water-sediment contact zone consists of three subzones: the suprabottom water, the fluffy layer, and the surface sediment. The total number, biomass, and integral activity of the microorganisms (dark 14CO2 assimilation) in the fluffy layer are usually higher than in the suprabottom water and sediment. The fluffy layer shows a decrease in the oxygen content and the growth of the dissolved biogenic elements. It was provided by the particulate organic matter supporting the vital activity of the heterotrophs from the overlying water column and by the flux of reduced compounds (NH4, H2S, CH4, Fe2+, Mn2+, and others) from the underlying sediments. The Corg isotopic composition of the fluffy layer and the sediments is 2–4 ‰ heavier than that of the particulate matter and sediment due to the presence of the isotopically heavy biomass of microorganisms. A change in the isotopic composition of the Corg in the fluffy layer and surface sediment as compared to the Corg of the particulate matter is a widespread phenomenon in the Arctic shelf seas and proves the leading role of microorganisms in the transformation of the particulate matter into sediment.