Submarine groundwater discharge (SGD) is a major process operating at the land-sea interface. Quantifying the SGD nutrient loads and the marine/terrestrial controls of this transport is of high importance, especially in oligotrophic seas such as the eastern Mediterranean. The fluxes of nutrients in groundwater discharging from the seafloor at Dor Bay (southeastern Mediterranean) were studied in detail using seepage meters. Our main finding is that the terrestrial, fresh groundwater is the main conveyor of DIN and silica to the coastal water, with loads of 500 and 560 mol/yr, respectively, per 1 m shoreline. Conversely, recirculated seawater is nutrient-poor, and its role is mainly as a dilution agent. The nutrient loads regenerated in the subterranean estuary (sub-bay sediment) are relatively small, consisting mostly of ammonium (24 mol/yr). On the other hand, the subterranean estuary at Dor Bay sequesters as much as 100 mol N/yr per 1 m shoreline, mainly via denitrification processes. These, and observations from other SGD sites, imply that the subterranean estuary at some coastal systems may function more as a sink for nitrogen than a source. This further questions the extent of nutrient contributions to the coastal water by some subterranean estuaries and warrants systematic evaluation of this process in various hydrological and marine trophic conditions.