The samples of water and bottom sediments of the East Siberian and Chukchi Seas collected during the second Russian-American RUSALCA expedition were used to analyze patterns of the isotopic composition of carbon in the organic matter (OM) of suspended material (SOM) and bottom sediments (BOM). Similar to other marine environments, the SOM isotopic composition depended on the ratio between the terrigenous and planktonic OM, both in the water body as a whole and in its parts. Thus, in the East Siberian Sea the carbon of SOM was poorer in 13C (δ13C = −24.51‰) than the open part of the more productive Chukchi Sea (δ13C = −22.16‰). In the less productive coastal waters of the Chukchi Sea, the ratio of terrigenous OM increased, resulting in a δ13C shift to lower values (−23.40‰). Due to the influx of reduced products of anaerobic diagenesis of the sediments, elevated total number of microorganisms and dark CO2 fixation were found in the near-bottom water at the water-sediment biogeochemical barrier. The newly formed biomass of autotrophic microorganisms shifted the carbon isotopic composition of the near-bottom suspended material to more positive δ13C values, with the average values of −23.39 and −20.37‰ for the East Siberian and Chukchi Sea, respectively. Changes in the carbon isotopic composition of OM resulting from microbial activity continued in the upper sediment layers. When the rate of biomass synthesis increased that of biomass consumption, the 13C content increased further. At higher rates of OM mineralization, 12C accumulated in its remaining part.