Submarine groundwater discharge (SGD)—including terrestrial freshwater, density-driven flow at the saltwater–freshwater interface, and benthic exchange—can deliver nutrients to coastal areas, generating a negative effect in the quality of marine water bodies. It is recognized that water stable isotopes (18O and 2H) can be helpful tracers to identify different flow paths and origins of water. Here, we show that they can be also applied when assessing sources of nutrients to coastal areas. A field site near a lagoon (Ringkøbing Fjord, Denmark) has been monitored at a metric scale to test if stable isotopes of water can be used to achieve a better understanding of the hydrochemical processes taking place in coastal aquifers, where there is a transition from freshwater to saltwater. Results show that 18O and 2H differentiate the coastal aquifer into three zones: Freshwater, shallow, and deep saline zones, which corresponded well with zones having distinct concentrations of inorganic phosphorous. The explanation is associated with three mechanisms: (1) Differences in sediment composition, (2) chemical reactions triggered by mixing of different type of fluxes, and (3) biochemical and diffusive processes in the lagoon bed. The different behaviors of nutrients in Ringkøbing Fjord need to be considered in water quality management. PO4 underneath the lagoon exceeds the groundwater concentration inland, thus demonstrating an intra-lagoon origin, while NO3, higher inland due to anthropogenic activity, is denitrified in the study area before reaching the lagoon.