Evaluating the sources of nutrient inputs to coastal lagoons is required to understand the functioning of these ecosystems and their vulnerability to eutrophication. Whereas terrestrial groundwater processes are increasingly recognized as relevant sources of nutrients to coastal lagoons, there are still limited studies evaluating separately nutrient fluxes driven by terrestrial groundwater discharge and lagoon water recirculation through sediments. In this study, we assess the relative significance of these sources in conveying dissolved inorganic nutrients (NO3−, NH4+ and PO43−) to a coastal lagoon (La Palme lagoon; France, Mediterranean Sea) using concurrent water and radon mass balances. The recirculation of lagoon water through sediments represents a source of NH4+ (1900–5500 mol d−1) and PO43− (22–71 mol d−1), but acts as a sink of NO3−. Estimated karstic groundwater-driven inputs of NO3−, NH4+ and PO43− to the lagoon are on the order of 200–1200, 1–12 and 1.5–8.7 mol d−1, respectively. A comparison between the main nutrient sources to the lagoon (karstic groundwater, recirculation, diffusion from sediments, inputs from a sewage treatment plant and atmospheric deposition) reveals that the recirculation of lagoon water through sediments is the main source of both dissolved inorganic nitrogen (DIN) and phosphorous (DIP) to La Palme lagoon. These results are in contrast with several studies conducted in systems influenced by terrestrial groundwater inputs, where groundwater is often assumed to be the main pathway for dissolved inorganic nutrient loads. This work highlights the important role of lagoon water recirculation through permeable sediments as a major conveyor of dissolved nutrients to coastal lagoons and, thus, the need for a sound understanding of the recirculation-driven nutrient fluxes and their ecological implications to sustainably manage lagoonal ecosystems.