Understanding the groundwater dynamics is very important for strategic management of the water resource as urbanization and population growth put South Africa’s current water supply under tremendous stress. The groundwater resources potential and quality characteristics of the greater Johannesburg area, was thoroughly assessed using hydrogeochemical and environmental isotope techniques. The results of the geochemical and stable isotope investigations help understand the groundwater setting. Mixing process of fresh and polluted water is taking place at shallow zones within the weathered crystalline rocks and dissolution cavities in dolomites, where the rocks are characterized by the lithological and structural complexities. Furthermore, it was confirmed that the solute composition of the water results from two basic contributions: the reaction of meteoric water with weathered zones in the near surface area and direct infiltration through dolomite dissolution cavities. The results further indicate that the dominant movement mechanism of ions is through a diffusive process, which could be due to the limited availability of fractures with depth and its possible sealing by calcite precipitation. Consequently, the provenance of groundwater circulation is limited to shallow depths, however, dissolution cavities, fractured and sheared zones allow deeper circulation of groundwater. Moreover, the natural water quality is found to be highly impacted by acid mine drainage which is derived from the gold mines in the Witwatersrand basin as it has been observed in previous studies.