South Africa is one of the water scarce nations and rated the 30th driest country on a global scale. This scenario necessitates scientific program across the country to augment and provide alternative to groundwater depletion leading to the inception of MAR system with a pilot-scale experimentation of artificial groundwater recharge in the Cape Flats region to meet water demand and rapid urbanization. The aim of this study was to conduct an overview of global and existing local managed aquifer recharge operations to present a sustainable method of investigation to support Polokwane MAR scheme operation. This paper proposes a way to improve Polokwane MAR scheme based on the present condition and operation. The study area lies within the Goud-plaats/ Hout River granitic gneiss with a composite aquifer consisting of a weathered zone and Alluvium Formation. Additionally, the water quality parameters distribution revealed high concentration of Na, Cl and Mg in the downstream of the study area with concentration value ranging from 140–170, 139–174 and 75–89 meq/L. The interpolated spatial distribution maps indicate that the downstream of the area is characterized by high Na, Cl, and Mg to a moderate and lower concentration trend of NO3, Ca, and Coliform. Finally, the study set an understanding of the Polokwane MAR scheme and implication of high groundwater recharge in the downstream and the needs to protect groundwater contamination and clogging during MAR operation.