South African karst aquifers are mainly associated with the dolomitic lithologies of the Transvaal Supergroup. Despite the socio-economic and environmental importance of these aquifers, no scientifically based methodology to outline areas that need protection from potential harmful activities exists. Thus an intrinsic resource aquifer vulnerability mapping method for karst terrains in South Africa was developed. The methodology is a modification of the COP aquifer vulnerability mapping method, developed by the Hydrogeology Group of the University of Malaga. The method is predominantly based on the capability of the unsaturated zone to filter or attenuate pollutants by different processes but considers two additional factors that either increase or reduce the protection provided by the unsaturated zone. These are surface conditions that control water flowing towards zones of rapid infiltration, and the temporal availability of a transport agent (rainfall). These three factors are combined to obtain a final vulnerability index, which is spatially visualised using five vulnerability classes (ranging from Very Low to Very High). Modifications to the original COP method include, amongst others, the consideration of rock types commonly found in South Africa, a statistical redefinition of high rainfall (wet) years, a revised consideration of rainfall rates to account for dilution processes and the consideration of older, sediment filled swallow holes. The method was applied to produce a vulnerability map for Cradle of Humankind World Heritage Site near Krugersdorp, South Africa. The vulnerability map clearly shows the generally inferior but variable aquifer protection in areas characterised by dolomitic lithologies, while surrounding non-karstic areas offer moderate to high resource protection. The proposed aquifer vulnerability mapping methodology should be used to assess karstic terrains during land use planning and environmental impact assessments. As an easily understandable planning tool the maps can reduce the likelihood of aquifer pollution.