The carbonate system was studied in different areas of the Sea of Japan and Sea of Okhotsk by measuring pH using a cell without liquid junction in the Pitzer's pH scale and measuring total alkalinity using the Bruevich's technique. The processes controlling the spatial and temporal dynamics of CO₂ sinks and sources are discussed for the areas of the Sea of Okhotsk and Sea of Japan: Amur River, Sakhalin Bay, Shantar's bays, open sea and Razdolnaya River, southwestern part of Peter the Great Bay, open sea, respectively. During the period when the rivers are not covered with ice, the annual CO₂ emission to the atmosphere as a result of respiration process in the rivers is 2.5×10⁴ tC and 4.5×10⁶ tC by Razdolnaya R. and Amur R., respectively. As result of weathering and photosynthesis processes, the annual CO₂ consumption from the atmosphere is -4.7×10⁴tC and -3.8×10⁶tC by ecosystems of Razdolnay R. and Amur R., respectively. River-dominated Ocean Margins – Amursky Bay (Sea of Japan) and Sakhalin Bay (Sea of Okhotsk) – were considered. Due to nutrient inputs from rivers and intensive photosynthesis, a biological pump which carries organic matter to the seafloor is formed, leading to seasonal hypoxia in the Amursky Bay and to the formation of the feeding area for gray whales on the Eastern Sakhalin Slope. The Ocean-dominated Margins – southwestern part of the Peter the Great Bay (Sea of Japan) and Shantar's Bays (Sea of Okhotsk) were considered. The southwestern part of Peter the Great Bay becomes a sink for atmospheric CO₂ after the seasonal upwelling event which supply nutrients. The water exchange between the Shantar's bays and the Sea of Okhotsk is piling up nutrients to the bays. The Shantar's Bays act as the sink for atmospheric CO₂ due to photosynthesis and cooling processes occurring in spring, while most of the area of the bays acting as the source of the CO₂ to the atmosphere through respiration and heating processes occurring in late summer. Based on underway observations most surface water along of the ship route in the Sea of Okhotsk is acting as the sink of atmospheric CO₂ through photosynthesis and as the source of CO₂ to the atmosphere in the Bussol Straight area due to intense vertical mixing. Observations showed that the north part of the Sea of Japan is a source of CO₂ to the atmosphere due to heating process in summer and deep convection in winter. The southern part of the Sea of Japan is a sink of atmospheric CO₂ due to photosynthesis and cooling processes. In general, the Sea of Japan reveals negative CO₂ emission in the period 1999 – 2014 due to global eutrophication caused by atmospheric NO₂ pollution.