In the central region of Chile, the Mega-Drought together with the demographic increase near the coast threatens groundwater availability and the hydrogeological functioning of coastal wetlands. To understand the hydric relationship between an aquifer and a wetland in a semi-arid coastal region of Central Chile (Valpara & iacute;so, Chile), as well as its geoenvironmental effects, four data collection campaigns were conducted in the wetland-estuary hydric system and surroundings, between 2021 and 2022, including physical, hydrochemical, and isotopic analyses in groundwater (n = 16 sites) and surface water (n = 8 sites). The results generated a conceptual model that indicates a hydraulic connection between the wetland and the aquifer, where the water use in one affects the availability in the other. With an average precipitation of 400 mm per year, the main recharge for both systems is rainwater. Three specific sources of pollution were identified from anthropic discharges that affect the water quality of the wetland and the estuary (flow from sanitary landfill, agricultural and livestock industry, and septic tank discharges in populated areas), exacerbated by the infiltration of seawater laterally and superficially through sandy sediments and the estuary, increasing salinity and electrical conductivity in the coastal zone (i.e., 3694 mu S/cm). The Del Sauce subbasin faces strong hydric stress triggered by the poor conservation state of the riparian-coastal wetland and groundwater in the same area. This study provides a detailed understanding of hydrological interactions and serves as a model for understanding the possible effects on similar ecosystems, highlighting the need for integrated and appropriate environmental management.