Dolomitic aquifers are regarded as important groundwater storage sites in South Africa. Since these aquifers occur in a semi-arid climatic setting with low rainfall, often characterized by a torrential downpour and high potential evapotranspiration, the occurrence of active recharge is very limited (<5% of mean annual rainfall) as compared with the rainfall amount. The Malmani dolomites that have undergone greenschist metamorphism contain widespread caves and open karst structures at shallow levels, which facilitate groundwater recharge, circulation, storage and spring occurrence. However, the open karst structures receive recharge that passes through fractures in the vadose zone, which regulates the recharge through retardation and mixing processes. The integrated approach involving major ions and stable isotopes of water was applied to understand the recharge mechanism. The cave drip water samples were represented by the δ18O values of −3.95‰ to 3.32‰ and the δ2H values ranging from −11.0‰ to 27.7‰. On the other hand, the rainfall isotope results for δ18O fall between −16.11‰ and 5.38‰, while the δ2H values fall between −105.7‰ and 35.6‰. The most depleted Malapa springs contain δ18O of −5.64‰ and δ2H of −32.4‰. Based on the results, the mixing of water in the vadose zone could be considered as an indicator of the dominance of a slow-diffusive flow process in the aquifer as a result of poor fracture permeability. However, regional groundwater circulation through faults and dykes besides interconnected karst structures helps in generating highly productive karst springs in the region characterized by low rainfall.