The interaction between surface water and groundwater is a complex process that can potentially deteriorate the quality of water, which is highly needed by communities. An environmental isotope and stream discharge based study has been conducted in the upper Crocodile River Basin, Johannesburg, which is characterized by fractured crystalline rocks and dolomitic aquifers from which groundwater is extracted for diverse economic activities. The seepage of mine water into a dolomitic aquifer in the vicinity of the Sterkfontein cave has been quantified and falls between 24 × 106 m3/y and 29 × 106 m3/y. The environmental isotope results also show that the decanting mine water extensively interacted with the shallow groundwater and streams. On the other hand, the dolomites (Malapa area) that lie away from mine areas in different dolomitic compartment contain uncontaminated and old groundwater with low 3H, which indicates long residence time, with depleted 18O and 2H indicating a recharge that took place prior to evaporation, and afterwards the recharged water circulated for long period of time. Streams also lose water into the dolomitc aquifer through sinkholes and fractures. Therefore, surface water and groundwater are intimately connected in the area.