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Identification of hydrogeologic controls on groundwater flowpaths, recharge, and salinization is often critical to the management of limited arid groundwater resources. One approach to identifying these mechanisms is a combined analysis of hydrogeologic and hydrochemical data to develop a comprehensive conceptual model of a groundwater basin. To demonstrate this technique, water samples were collected from 33 discrete vertical zone test holes in the Hueco Bolson aquifer, located within the Trans-Pecos Texas region and the primary water resource for El Paso, Texas, USA and Juarez, Mexico. These samples were analyzed for a suite of geochemical tracers and the data evaluated in light of basin hydrogeology. On the basis of delta H-2 and delta O-18 data, two regional recharge sources were recognized, one originating from western mountain-fronts and one from through-flow of the adjacent Tularosa aquifer. Chloride concentrations were strongly correlated with lithologic formations and both Cl/Br and Cl-36 ratios suggested the primary chloride source is halite dissolution within a specific lithologic unit. In contrast, sulfur isotopes indicated that most sulfate originates from Tularosa basin Permian gypsum sources. These results yielded a more comprehensive conceptual model of the basin, which suggested that chloride salinization of wells is the result of upconing of waters from the Fort Hancock formation.