Shelf seas are among the most active biogeochemical marine environments and the East Siberian Arctic shelf (ESAS) is a prime example. We examined the carbonate system dynamics and CO2 fluxes in the ESAS based on our multi-year study (2002-2011). It is usually assumed that at high latitudes important CO2 absorption from atmosphere occurs during the ice free period when primary production is high and water temperature is low. However our data show that during summer-fall season a significant part of the shallow East-Siberian Sea and the eastern Laptev Sea serve as a strong source of CO2 to the atmosphere. We classified this near-shore ecosystem as mainly heterotrophic (i.e. net production of inorganic carbon) and the main source of allochthonous OC is a terrestrial labile OC mobilized from the degrading permafrost. Riverine waters are additional significant source of carbon. The average CO2 emission during summer season was ranged between 1 mmol/(m??day?) and 10 mmol/(m? day?). On the contrary, the Chukchi Sea is an autotrophic province and a strong sink for atmospheric CO2. It was found that the direction of fluxes changes near the frontal zone between “freshened/source” and “Pacific/sink” waters and this zone’s position varies significantly from year to year. It is mainly attributed to the difference in atmospheric circulation patterns driven the Arctic Ocean circulation. This work was supported by the Government of the Russian Federation (megagrant No. 14.Z50.31.0012).