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The quality of the groundwater supplying drinking water to the Guadalajara metropolitan area has deteriorated due to both endogenic and exogenic processes. Previous studies of this complex neotectonic volcanic environment suggest that the sources of contamination here are underground fluids derived from an active volcanic center and surface wastewater derived from regional land-use intensification. This study uses isotopic, gaseous, and chemical signatures to more comprehensively characterize this groundwater flow and its contamination paths. Groundwater is mainly recharged at the La Primavera Caldera to the west and is discharged into the Santiago River to the east. The exception to this trend is the Toluquilla area, where groundwater most likely represents rainfall originating from outside the basin limits. Evaporation affects groundwater in these areas, especially waters that have been affected by recycling below urban areas in the Atejamac area and by intensive agricultural activity in the Toluquilla area. Additionally, we present evidence that groundwater flow through alluvial sediments and tuffs in deeper wells mixes with a lower aquifer unit in basaltic-andesitic rocks, which are in contact with hydrothermal fluids. Groundwater ages range from postbomb in the western and northwestern regions of the study area (i.e., the Atemajac aquifer unit) to Late Pleistocene in the southern and southeastern regions (i.e., the Toluquilla aquifer unit). Recently recharged water records little mixing and is located mostly in or near the La Primavera volcanic system. As groundwater undergoes gravitational flow towards discharge areas, it mixes with older water components. Chloride and sodium concentrations above natural background levels are primarily related to volcanic activity, nitrate is associated with human activities, and sulfate originates from both anthropogenic sources and water-rock interactions. Nitrate originating from land-use activities (such as sewers, septic tanks, landfills, and agricultural fields) that is introduced into the deeper part of the groundwater system is expected to travel with the groundwater to the discharge areas because oxidizing conditions will prevent microbial reduction. See Supplementary Information. [ABSTRACT FROM AUTHOR]