Coastal and shelf carbonate chemistry of the East China Sea is strongly influenced by physical and biological processes often over short time periods. In order to better understand the tight coupling between coastal physics, pelagic plankton production and carbon biogeochemistry, we followed a drogued patch in two regions to the south and north of the Changjiang River estuary over a three week period in May 2017. We report here modifications in marine carbonate chemistry in relation to rapid changes in phytoplankton and nutrient fields. pH varied from 7.932 ~ 8.268 in the southern region of the Changjiang River estuary and from 7.911 ~ 8.471 in the northern region. High pH values were detected in the surface with relative high phytoplankton biomass. The pH value would increase by an average about 0.2 pH units in high productivity regions. The partial pressure of CO2 (pCO2) had a similar distribution as the total dissolved inorganic carbon (CT), which was opposite to the varying trend of pH. In the high productivity regions, pCO2 and CT values would decrease. AT ranged from 2181μmol/kg ~ 2262μmol/kg in the southern study region and from 2132μmol/kg ~ 2264μmol/kg in the northern study region, with such a distribution trend, high AT values were detected in the bottom and low values were distributed in the surface. In the surface layer, AT values varied narrowly when the phytoplankton biomass changed greatly, because it is not directly affected by biological processes. Relationships between carbonate parameters and environmental factors were studied through the Pearson Correlation Analysis and multiple linear regressions (MLRs). Better relationships were found between AT and salinity (P < 0.01), pH and nutrients, Chl-a, confirming the big influences of physical and biological processes.