In highly anthropized watersheds, surface water tributaries may carry unexpected high quantities of radon and radium to coastal lagoons. Investigating submarine groundwater discharge (SGD) with radionuclide tracers is therefore a complex task. In order to quantify SGD and decipher the influence of the different water sources, we combined a radon (222Rn) and radium (223Ra, 224Ra) survey with the hydrodynamic modeling of a lagoon. We applied it to the Mar Menor lagoon (SE Spain) where surface water tributaries and undocumented emissaries carry water from groundwater drainage and brines from groundwater desalinization. We identified the areas of influence of the plume of radionuclides from the river, located major areas of SGD and proposed a location for two submarine emissaries. Groundwater from underlying sediments was selected as the best representative SGD end member, compared to groundwater from piezometers. Mass balances in winter and summer seasons provided yearly SGD fluxes of water of 7.2-15.9 108 m3/y (222Rn), 21.9-44.7 108 m3/y (224Ra) and 6.9 108 m3/y (223Ra, measured in winter only). The difference between values for 222Rn was explained by the different temperature and wind conditions. Tidal pumping was identified as a main driver for recirculated saline groundwater, while fresh submarine groundwater discharge from the aquifer was about 1% of total SGD.