Clarifying the complex physical-chemical-biological interactions is essential for evaluating the carbon dioxide partial pressure (pCO₂) in coastal waters. In the coastal water of the Pearl River Estuary, the seasonal variations and spatial differences in the carbonate system are more pronounced compared to the inner estuary and off-shore waters. To understand the controlling factors of the pCO₂, a three-dimensional coupled physical-biogeochemical model is implemented to address the temporal and spatial characteristics of the pCO₂ in the coastal water of the Pearl River estuary. The results show that the sea surface temperature plays a key role in the temporal and spatial distribution of pCO₂ in winter, with coastal water pCO₂ significantly lower than atmospheric. In summer, non-temperature effects influence pCO₂ in coastal water with biological processes reducing the surface pCO₂, and pCO₂ fluctuates significantly primarily influenced by stratification. Biological processes and stratification affect the spatial distribution of surface pCO₂ during summer, and lower seawater pCO₂ exists in the areas that are greatly influenced by freshwater. In the coastal water of the Pearl River Estuary, the air-sea CO₂ fluxes showed a strong sink for CO₂ in winter with a flux of -4.06 ± 0.13 mmol m^-2 d^-1 and a weak sink in summer with a flux of -1.40 ± 0.29 mmol m^-2 d^-1.
 

partial pressure of CO2 (pCO2), numerical model, biological process, sea surface temperature