Climate models for the 21st century project further reduction in the warm season precipitation and more frequent droughts across Mexico. In the possible scenario of enhanced aridity from global warming, the δ18O (−10.6 to −6.3 ‰) and δ2H (−71.1 to −57.1 ‰) compositions and deuterium-excess (0.2–14.6‰) of shallow groundwater from two different basins (Sandia and El Potosi) with similar geological and geomorphological settings were considered to evaluate the influences of early summer rainfall and later summer tropical storms on aquifers at water-scarce southeast margin of the Chihuahuan Desert. Groundwater of the Sandia Basin was recharged mainly from tropical storms. Higher CO2 partial pressure (log pCO2: −2.70 to −1.61) caused more gypsum dissolution (Ca–Mg–SO4 facies) and the effect of irrigation return flow (Ca–Mg–Cl facies) was minor. Even though the El Potosi Basin is in proximity, its groundwater was recharged from both the early and late summer precipitations. The multivariate factor analysis helped to separate the process of rock-water interactions from the recharge seasonality. Gypsum dissolution was less as the partial pressure of CO2 was comparatively lower (log pCO2: −3.01 to −2.15), and the ion exchange along with carbonate mineral dissolutions led to Ca–Mg–HCO3 facies. Over-exploitation under the condition of reduced warm season rainfall would continue to enhance the salinity of groundwater in this region. Hence, the drought mitigation policies should prioritize sustainability of the depleted aquifers and cultivation of salinity resistant crops.