In this study, a land-estuarine-ocean biogeochemical modeling system has been developed for the Pearl River Estuary and the adjacent Northern South China Sea in the Guangdong-Hong Kong-Macao Greater Bay Area (China-GBA) to investigate the spatiotemporal variability and mechanisms controlling pCO₂ and sea-air CO₂ fluxes in key oceanic regions. Sensitivity experiments were conducted to isolate the effects of changes in (1) biological activities; (2) riverine material loadings; and (3) atmospheric carbon dioxide (CO₂) levels. The results indicate that (1) Lingding Bay (LDB) and the Annual Plume Zone (APZ) act as sources of atmospheric CO₂, while the Summer Plume Zone (SPZ) and the Yuedong Upwelling Zone (YUZ) performed as sinks. This is attributed to biological respiration in LDB and APZ exceeding primary production, as high suspended sediment concentrations hinder light penetration; (2) Compared to the historical period, changes in terrestrial material input over the past 60 years have  significantly increased CO₂ emissions from LDB and APZ, primarily through increases in total alkalinity (TA), whereas the impact  on SPZ and YUZ  was negligible; (3) The increase in atmospheric CO^_₂ concentration reduces CO₂ emissions in LDB and APZ while converting SPZ and UPZ from carbon sources into carbon sinks, mainly by regulating dissolved inorganic carbon (DIC). This study reveals the spatial heterogeneity of carbon source/sink in the key oceanic areas of China-GBA due to internal (biological activities) and external drivers (human activities and climate change) providing a significant theoretical foundation for implementing effective marine carbon dioxide removal strategies (e.g. wastewater alkalinity addition) under the framework of the ONCE program.