The intense biogeochemical reactivity of the freshwater-seawater mixing interface inside coastal aquifers (also called subterranean estuaries; STEs) alters the chemical composition of groundwater before its discharge into coastal waters. However, human activities on land and at the shore may also alter the role of STEs as chemical modulators in the land-to-ocean transfer of solutes. Here, we evaluate how these systems transform the composition of anthropized and pristine continental groundwaters by examining the levels and reactivity of oxygen, nutrients and dissolved organic matter (DOM) quantity and quality in porewaters of two urban STEs (one internally oxygenated due to a human-derived gravel layer and the other anoxic) and one from a local National Park considered pristine but under similar geological, hydrological and oceanographic contexts and comparing them with the composition of the surrounding continental groundwaters. Continental groundwaters surrounding urban STEs exhibited nitrate levels two orders of magnitude higher than those from the National Park, while the latter doubled DOM levels compared to the urban sites. This contrast was reflected in the composition of the terrestrial freshwater discharge tube entering STEs, enriched with DOM in the pristine STE and with nitrate in the oxygenated urban STE. Yet, comparison between measured concentrations and conservative mixing lines revealed that most DOM was produced within the pristine STE. No groundwater-borne nitrate was detected in the anoxic urban STE interior, which contrasted with the enhanced nitrogen transport through the gravel layer of the oxygenated urban STE. Close to the seepage face, interaction between terrestrial brackish groundwater and the oxygen and coastal organic matter sourced by tidally-driven recirculated seawater fueled the production of phosphate, dissolved inorganic nitrogen and aromatic DOM through benthic reactivity. This study reveals how despite anthropogenic impacts on continental groundwaters, the biogeochemistry of STEs is the main driver of the composition of the discharged porewater.