Groundwater/surface-water interaction is receiving increasing focus in Africa due to its importance to ecologic systems and sustainability. In South Africa’s 1998 National Water Act (NWA), water-use licenses, including groundwater, are granted only after defining the Reserve, the amount of water needed to supply basic human needs and preserve some ecological integrity. Accurate quantification of groundwater contributions to ecosystems for successful implementation of the NWA proves challenging; many of South Africa’s aquifers are in heterogeneous and anisotropic fractured-rock settings. This paper reviews the current conceptualizations and investigative approaches regarding groundwater/surface-water interactions in the context of South African policies. Some selected pitfall experiences are emphasized. The most common approach in South Africa is estimation of average annual fluxes at the scale of fourth-order catchments (∼500 km2) with baseflow separation techniques and then subtracting the groundwater discharge rate from the recharge rate. This approach might be a good start, but it ignores spatial and temporal variability, potentially missing local impacts associated with production-well placement. As South Africa’s NWA has already been emulated in many countries including Zambia, Zimbabwe and Kenya, the successes and failures of the South African experience dealing with the groundwater/surface-water interaction will be analyzed to guide future policy directions.