The salt chemical industrial base of Guyuan is located in the south of Ningxia, northwestern China. Guyuan had been not only an important but also a challenging area for the state’s poverty alleviation and development work for a long time. In addition, the overexploitation of groundwater for agriculture activities in recent decades had led to the decline of the water table and the degradation of the water quality. In this study, environmental isotope data for different water sources are presented and discussed to identify the hydrochemical character of the aquifer systems and to investigate the geochemical processes controlling groundwater mineralization. Piper trilinear diagrams indicate that shallow groundwater in the western mountainous area is characterized by three water types (i.e., SO4–HCO3, HCO3–SO4, and SO4) while deep groundwater is characterized by two water types (i.e., SO4 and SO4–Cl). Furthermore, hydrochemical tracers show that the groundwater in the Qingshuihe plain is of the (1) HCO3–SO4 and HCO3 types in the southern piedmont recharge zone, (2) SO4 type in the southwestern recharge zone, (3) SO4–HCO3 and HCO3–SO4 types in the midwestern recharge zone, (4) SO4–HCO3 and SO4–Cl–HCO3 types in the northwestern recharge zone, and (5) SO4–HCO3, HCO3–SO4, and SO4 types in the runoff and discharge zone. Dissolution of soluble salts is the principal contributor to the water geochemistry in the western mountainous area within the study region. However, water geochemistry in the Qingshuihe plain is primarily controlled by mixing processes and by the recharge of highly mineralized surface water and groundwater in the southwestern and northwestern piedmont areas. In the conventional δD and δ 18O diagram, the distribution of data points indicates that the groundwater is of meteoric origin and has been affected by evaporation before or during underground transit. The deep groundwater in the western mountainous area is recharged under conditions that are different from currently prevailing conditions.