Organophosphate esters (OPEs) are ubiquitous marine contaminants that globally concerned. While surface inputs are well-studied, the role of subsurface transport remains poorly constrained. Submarine groundwater discharge (SGD) is a key conveyer driving seawater-groundwater interactions on the benthic ocean boundary, which impacts on OPEs’ behavior have been overlooked. This study comprehensively investigates the distribution, transport mechanisms and sources of OPEs from coastal groundwater to seawater in the Beibu Gulf, China. Distinct OPEs concentration gradients were found, which ranked as groundwater > tidal flat porewater > seawater, while the high compositional similarity indicated a shared terrestrial origin among three  water matrix. Strong correlations (p < 0.01) and principal component analysis overlap confirmed the partial inheritance of groundwater signatures by seawater, highlighting the porewater as a dynamic biogeochemical reactor. Crucially, coupling OPEs with environmental parameters and dissolved organic matter (DOM) fingerprints revealed how SGD drives OPEs cycling in the coastal ocean.  For the first time, this work not only highlights SGD as a crucial, previously underestimated pathway for OPEs in coastal sea, but also provides novel mechanistic insights into how DOM dynamics regulate the fate of emerging contaminants across the land-ocean interface.