The composition of submarine groundwater discharge (SGD) is strongly influenced by reactions occurring within subterranean estuaries where fresh groundwater and seawater mixes. Redox conditions play a critical role in several of these reactions and, therefore, can regulate the fate of both land- and marine-derived chemicals in subterranean estuaries. Redox conditions within subterranean estuaries largely depend on the transit times of both fresh and saline groundwater, which are affected by the permeability and heterogeneity of the beach matrix. This study aims to evaluate how heterogeneous sediment layers influence transit times and nutrient cycling within a subterranean estuary, and the effect on nutrient fluxes to the ocean. To achieve this, we combined field data with numerical reactive transport modeling conducted using SEAWAT-PHT3D. Field data from Panxón Beach (Ría de Vigo, NW Iberian Peninsula) reveals the presence of a highly permeable gravel layer at 1-2 m depth, likely formed from the burial of anthropogenic materials. Combined field and modeling results show that the gravel layer decreases groundwater transit times and increases internal oxygenation, which in turn promotes aerobic respiration of marine-derived organic matter and increases dissolved inorganic nitrogen concentrations. Sensitivity simulations show that the location and thickness of high permeability layers influence the internal oxygenation and nutrient cycling within the subterranean estuary. This study highlights the importance of sediment heterogeneity on the final chemical composition of SGD.