With the increasing population, urbanization and industry in the arid area of Tecate, there is a concomitant increase in contaminants being introduced into the Tecate River and its aquifer. This contamination is damaging the usable groundwater supply and making local residents and commercial enterprises increasingly dependent on imported water from the Colorado River basin. In this study we apply a suite of chemical and isotopic tracers in order to evaluate groundwater flow and assess contamination trends. Groundwater recharge occurs through mountain-block and mountain-front recharge at higher elevations of the ranges. Groundwater from the unconfined, alluvial aquifer indicates recent recharge and little evolution. The increase in salinity along the flow path is due to interaction with weathering rock-forming silicate minerals and anthropogenic sources such as urban wastewater, residual solids and agricultural runoff from fertilizers, livestock manure and/or septic tanks and latrines. A spatial analysis shows local differences and the impact of the infiltration of imported waters from the Colorado River basin. The general trend of impaired water quality has scarcely been documented in the last decades, but it is expected to continue. Since the groundwater system is highly vulnerable, it is necessary to protect groundwater sources.