Submarine groundwater discharge (SGD) serves as a crucial pathway for terrestrial carbon transport to the ocean. However, our understanding of SGD's contribution to carbon dynamics and biogeochemical processes remains limited. Here, we used the radium quartet to estimate SGD in Daya Bay (China) across seasons and then applied dissolved carbon budget models for dissolved inorganic carbon (DIC) and dissolved organic carbon (DOC) to assess carbon sources and sinks and quantify SGD-derived carbon fluxes. The buffering capacity against ocean acidification and associated biogeochemical processes within the carbonate system was analyzed. SGD-derived DIC flux was 19–39 times that of local riverine input in autumn, and 27–66 times that of local riverine input in spring. SGD-derived DOC flux ranged from 2 to 6 times that of local riverine input in autumn and from 2 to 8 times in spring. Further, the biogeochemical processes regulating carbon components in seawater exhibited significant seasonal characteristics. Primary production and CO2 outgassing were predominant in spring, associated with higher biological activity and calmer wind conditions. With lower primary productivity and enhanced remineralization in autumn, 37.5% of seawater samples might have undergone organic matter degradation and carbonate dissolution. Moreover, groundwater exhibited a buffering capacity across different seasons, with higher values observed in nearshore seawater during autumn and offshore seawater during spring. The buffering capacity of nearshore seawater was affected by coastal groundwater, exhibiting significant deviations relative to offshore seawater. This study emphasizes the essential role of SGD in coastal carbonate systems and reveals the seasonal characteristics in biogeochemical processes, buffering capacity, and environmental implications.