The Kara Sea is an area uniquely suitable for studying processes in the river-sea system. This is a shallow sea, into which two great Siberian rivers, Yenisei and Ob, flow. From 1995 to 2003, the sea was studied by six international expeditions onboard the R/V Akademik Boris Petrov. This publication summarizes the results obtained, within the framework of this project, at the Vernadsky Institute of Geochemistry and Analytical Chemistry, Russian Academy of Sciences. Various hydrogeochemical parameters, concentrations and isotopic composition of organic and carbonate carbon of the sediments, plankton, particulate organic matter, hydrocarbons, and dissolved CO2 were examined throughout the whole sea area at more than 200 sites. The d13C varies from -22 and -24 per mil where Atlantic waters enter the Kara Sea and in the north-eastern part of the water area to -27 per mil in the Yenisei and Ob estuaries. The value of d13C of the plankton is only weakly correlated with the d13C of the organic matter from the sediments and is lower by as much as 3-4 per mil. The paper presents the results obtained from a number of meridional river-sea profiles. It was determined from the relations between the isotopic compositions of plankton and particulate matter that the river waters carry material consisting of 70% detrital-humus matter and 30% planktonogenic material in the river part, and the material contained in the offshore waters consists of 30% terrigenous components, with the contribution of bioproducers amounting to 70%. The carbon isotopic composition of the plankton ranges from -29 to -35 per mil in the riverine part, from -28 to -27 per mil in the estuaries, and from -27.0 to -25 per mil in the marine part. The relative lightness of the carbon isotopic composition of plankton in Arctic waters is explained by the temperature effect, elevated CO2 concentrations, and long-distance CO2 supply to the sea with river waters. The data obtained on the isotopic composition of CO2 in the surface waters of the Kara Sea were used to map the distribution of d13C. The complex of hydrocarbon gases extracted from the waters included methane, C2-C5, and unsaturated C2=-C4= hydrocarbons, for which variations in the concentrations in the waters were studied along river-estuary-sea profiles. The geochemistry of hydrocarbon gases in surface fresh waters is characterized by comparable concentrations of methane (0.3-5 µl/l) and heavier hydrocarbons, including unsaturated ones. Microbiological methane with d13C from -105 to -90 per mil first occurs in the sediments at depths of 40-200 cm. The sediments practically everywhere display traces of methane oxidation in the form of a shift of the d13C of methane toward higher values and the occurrence of autogenic carbonate material, including ikaite, enriched in the light isotope. Ikaite (d13C from -25 to -60 per mil) was found and examined in several profiles. The redox conditions in the sediments varied from normal in the southern part of the sea to highly oxidized along the Novaya Zemlya Trough. Vertical sections through the sediments of the latter exemplify the complete suppression of the biochemical activity of microorganisms. Our data provide insight into the biogeochemistry of the Kara Sea and make it possible to specify the background values needed for ecological control during the future exploration operations and extraction of hydrocarbons in the Kara Sea.