Due to the complex physical and biogeochemical conditions, the adjacent South Yellow Sea (SYS) and East China Sea (ECS) are ideal sites for studying different carbonate characteristics in marginal seas. The distributions of carbonate system parameters were investigated in this region in early spring and summer. Overall, dissolved inorganic carbon (DIC) and alkalinity concentrations in the SYS were higher than those in the ECS due to the Yellow River runoff which was featured with intensive carbonate weathering and erosion. Low DIC, alkalinity and high pH values were observed in the Zhe-Min Coastal Current with intensive primary production in spring caused by the Changjiang River and Taiwan Warm Current. Temperature and biological activities were the primary drivers in controlling the partial pressure of CO2 (pCO2) variability in the SYS, whereas temperature was the only dominant factor in the outer shelf of the ECS, which was heavily impacted by the Kuroshio Current. The pCO2 dynamics was controlled by primary production and physical mixing in the Changjiang River plume and the inner and middle shelves of the ECS, due to the influence of the Changjiang River with high nutrient supply. Overall, strong CO2 sinks (-4.11 ± 5.28 mmol m-2d-1) turned into weak sources (0.88 ± 5.09 mmol m-2d-1) in the entire study area from spring to summer. Specifically, the SYS and ECS offshore waters changed from CO2 sinks in spring to sources in summer, while the Changjiang River plume always served as a CO2 sink.