Abstract. To better understand biogeochemical processes controlling CO₂ dynamics in those eutrophic large-river estuaries and coastal lagoons, we investigated surface water carbonate system, nutrients, and relevant hydrochemical parameters in the inner Changjiang (Yangtze River) Estuary, covering its channel-like South Branch and the lagoon-like North Branch, shortly after a spring-tide period in April 2010. In the North Branch, with a water residence time of more than 2 months, biogeochemical additions of ammonium (7.4 to 65.7 μmol kg⁻¹) and alkalinity (196 to 695 μmol kg⁻¹) were detected along with high salinity of 4.5 to 17.4. In the South Branch upper-reach, unusual salinity values of 0.20 to 0.67 were detected, indicating spillover waters from the North Branch. The spillover waters enhanced the springtime Changjiang export fluxes of nutrients, dissolved inorganic carbon, and alkalinity. And they affected the biogeochemistry in the South Branch, by lowering water-to-air CO₂ flux and continuing the nitrification reaction. In the North Branch, pCO₂ was measured from 930 to 1518 μatm at the salinity range between 8 and 16, which was substantially higher than the South Branch pCO₂ of 700 to 1100 μatm. Based on field data analyses and simplified stoichiometric equations, we suggest that the North Branch CO₂ productions were quantified by biogeochemical processes combining organic matter decomposition, nitrification, CaCO₃ dissolution, and acid-base reactions in the estuarine mixing zone. Although our study is subject to limited temporal and spatial coverage of sampling, we have demonstrated a procedure to quantificationally constrain net CO₂ productions in eutrophic estuaries and/or coastal lagoons, by coupling the chemical dynamics of carbonate and dissolved inorganic nitrogen systems.