Recharge mechanisms and the hydrochemical evolution of groundwater in a semi-arid, 6,840-km2, intermountain basin in central Mexico were investigated using stable isotopes and major chemical constituents. Ionic ratio analysis helped to conceptualize and quantify in part the subsequent geochemical evolution in the aquifer system. Mass balance models (PHREEQC) were used to interpret and rectify the geochemical properties of the aquifer. The recharge conditions have not changed noticeably during the last several thousands of years. The recharge mechanisms are accompanied by leaching of meteoric salts on and near the ground surface during major rain events, which previously accumulated after minor rain events. Rapid and diffuse infiltration can be excluded. Indirect infiltration from wadis (arroyos) and depressions (playas) with little mixing in shallow groundwater contrasts with a high degree of mixing for water with deep circulation. The prevailing source of major cations (ca2+, Mg2+, Na+, K+ is weathering of carbonates and albite, followed by exchange reactions on clays and hydroxides. Ca2+/Na+ exchange may interchange along the flow path with reverse (Na+/Ca 2+) exchange, although the Ca2+/Na + option is prevalent. Meteoric Ca and Mg inputs are relatively small; however meteoric Na is insignificant. Irrigation return flow plays an important role in the western part of the study area, giving rise to elevated sulfate and chloride concentrations.