Determining the origin of groundwater in active and unstable mining environments has proven quite challenging. We evaluated the origin and salinity of the groundwater using major/minor ions, H-2 and O-18 stable isotopes, and H-3 and C-14 radioisotopes. Samples were collected from a multi-aquifer system including three distinct aquifers: an upper alluvial aquifer (UAA), a lower alluvial aquifer (LAA), and a hard-rock aquifer (HRA). The water facies for most of the samples were Na-Cl with total dissolved solid concentrations ranging from 1.1 g L-1 in the freshwater of the Kheirabad aquifer (KhA), 148.8 g L-1 in the brines of the HRA, and 321 g L-1 in a salt playa. The unique ionic relationships between the ions imply the salinity mainly originates from halite dissolution. Moreover, the groundwater of HRA and LAA was altered by reverse cation exchange. Although the stable isotope data suggested a modern meteoric water source for the KhA samples, the UAA, LAA, and HRA groundwaters were significantly enriched relative to the local meteoric water line. Dating with H-3 and C-14 radioisotopes confirmed the characteristic differences between the aquifers with ages of 6200 (UAA), 18,000 (LAA), and 27,500 years (HRA), which ultimately supported their varied origins. Consequently, a regional conceptual flow model was developed based on the geological settings, stratigraphic evidence, hydrochemistry, and isotopic properties, which suggests that the UAA, LAA, and HRA were due to three transgressions of inland lakes 6200, 18,000, and 27,500 ago, respectively.