Coastal aquifers act as dynamic interfaces between terrestrial and marine systems, regulating the exchange of water and solutes through submarine groundwater discharge (SGD). While riverine fluxes of dissolved inorganic carbon (DIC) and total alkalinity (TA) have been extensively studied, the contributions of both fresh groundwater discharge and recirculated seawater remain poorly constrained. These overlooked pathways are particularly relevant in the context of saltwater intrusion (SWI), where mixing processes and biogeochemical transformations within subterranean estuaries reshape coastal carbon fluxes. By compiling and analyzing a global dataset of coastal groundwater compositions, we quantify DIC and TA fluxes via both fresh SGD and saline recirculation. Our findings reveal that SGD delivers DIC and TA to the ocean at magnitudes comparable to riverine inputs, with global DIC fluxes from SGD estimated at 3.6 ± 0.6 Tmol y⁻¹ (15–30% of the riverine flux) and TA fluxes at 2.6 ± 0.5 Tmol y⁻¹ (~10% of the riverine contribution). Notably, DIC concentrations frequently exceed TA due to non-conservative behavior in subterranean estuaries, highlighting the complex interplay between hydrological mixing, carbonate dissolution, and microbial activity. A key innovation in our approach is the simultaneous evaluation of TA and DIC in the same groundwater samples, allowing for a refined understanding of how SWI influences carbon cycling in coastal aquifers. By distinguishing flux contributions based on aquifer lithology, we provide new insights into the abiotic and biotic drivers of carbonate system variability. These results underscore the need to integrate SGD processes into global carbon budget models and further explore their role in modulating marine biogeochemistry.