In the frameworks of the program “Ecosystems of the Siberian Arctic seas”, carried out by Shirshov Institute of Oceanology RAS since 2007, studies of the structure of waters, spatial variability of the carbonate system parameters have been performed, and the intensity and direction of the carbon dioxide flux over the continental slope of the Laptev Sea and in the Vilkitsky Strait in September 2018 have been calculated. The presence of several main water masses that determine the structure of waters in the study area is shown. A strong spatial variability of the parameters of the carbonate system of sea waters, determined by the complexes of physical and chemical-biological processes, has been revealed. The intensity and direction of the carbon dioxide flux at the water–atmosphere boundary were calculated, ranging from –12 to +4 mmol m–2 day–1. It was revealed that the investigated area of the outer shelf of the sea and the continental slope of the Laptev Sea is an emitter of carbon dioxide into the atmosphere as of September 2018. The area of the Vilkitsky Strait, on the contrary, is an area of absorption of CO2.