Endorheic or closed drainage basins in arid and semi-arid regions are vulnerable to pollution. Nonetheless, in the freshwater-saltwater interface of endorheic saline lakes, oxidation-reduction (redox) reactions can attenuate pollutants such as nitrate (NO). This study traces the ways of nitrogen (N) removal in the Pétrola lake-aquifer system (central Spain), an endorheic basin contaminated with NO (up to 99.2mg/L in groundwater). This basin was declared vulnerable to NO pollution in 1998 due to the high anthropogenic pressures (mainly agriculture and wastewaters). Hydrochemical, multi-isotopic (δO, δN, δC, δO, and δH) and geophysical techniques (electrical resistivity tomography) were applied to identify the main redox processes at the freshwater-saltwater interface. The results showed that the geometry of this interface is influenced by land use, causing spatial variability of nitrogen biogeochemical processes over the basin. In the underlying aquifer, NO showed an average concentration of 38.5mg/L (n=73) and was mainly derived from agricultural inputs. Natural attenuation of NO was observed in dryland farming areas (up to 72%) and in irrigation areas (up to 66%). In the Pétrola Lake, mineralization and organic matter degradation in lake sediment play an important role in NO reduction. Our findings are a major step forward in understanding freshwater-saltwater interfaces as reactive zones for NO attenuation. We further emphasize the importance of including a land use perspective when studying water quality-environmental relationships in hydrogeological systems dominated by density-driven circulation.