Near-shore and direct groundwater inputs are frequently omitted from nutrient budgets of coastal lagoons. This study investigated groundwater-driven dissolved inorganic nitrogen (DIN) inputs from an alluvial aquifer to the hypertrophic Or lagoon, with a focus on the Salaison River. Piezometric contours revealed that the Salaison hydrogeological catchment is 42% bigger than the surface watershed and hydraulic gradients suggest significant groundwater discharge all along the stream. Hydrograph separation of thewater flowat a gauging station located 3 km upstream from the Or lagoon combined with DIN historical data enabled to estimate that groundwaterdriven DIN inputs account for 81–87% of the annual total DIN inputs to the stream upstream from the gauging station. A radon mass balancewas performed for the hydrological cycle 2017–2018 to estimate groundwater inflow into the downstream part of the stream. Results showed that (1) DIN fluxes increased by a factor 1.1 to 2.3 between the gauging station and the Salaison outlet, (2) the increase in DINwas due to two groundwater-fed canals and to groundwater discharge along the stream, the latter represented 63–78% of the water flow. This study thus highlights the significance of groundwater driven DIN inputs into the Salaison River, which account for 90% of the annualDINinputs. This is particularly true in the downstreampart of the river,which, on averages, supplies 48% of total DIN inputs to the river. These downstream DIN inputs into the Or lagoon were previously not taken into account in the management of this and other Mediterranean lagoons. The inputs will probably affect restoration processes for many years due to their residence timein the aquifer. This study throws light on a rarely documented source of ‘very-nearshore’ groundwater discharge to coastal streams in water and nutrient budgets of coastal zone ecosystems.