Chemical and isotopic data were used to explain the geochemistry and the hydrothermal influence in a groundwater system in Guadalajara, México. According to the measured parameters and the characteristics of the groundwater, four water groups were identified: i) thermal waters with high temperatures and high concentrations of Cl, Na, HCO3 and the presence of Li, Mn, F and Mg, apparently of old age with a long residence time; ii) mixed waters of Na-HCO3 to HCO3 water type, which represent a mixture of cold water and thermal water; iii) polluted water characterized by high concentrations of nitrate and sulfate derived from urban and agricultural return flow; iv) cold water characterized by low temperature values, low concentration of Cl, Na and salinity, of Na-HCO3 type. This last group represents modern water located in the recharge zone. Finally, major proportions of hydrothermal fluids are largest in the well waters of the first group varying from 1.9 to 12.5%. The other groups show hydrothermal fractions below 1.7%. Groundwater with elevated hydrothermal proportions is located to the southeastern area of the Toluquilla aquifers. This study identifies some processes that govern the groundwater and hydrothermal mixing.