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Towns along the West Coast of South Africa are facing water shortages due to climate change and increasing water demand. Managed aquifer recharge (MAR) is considered as a solution to improve water security. This paper presents a two-step method of combining geographic information system (GIS) based analysis with numerical modeling to select suitable sites for implementing MAR in the West Coast area. Many factors were taken into account to generate the initial map for suitable sites through GIS based analysis. Subsequently, groundwater flow modeling was adopted to verify and optimize the suitable sites selected by GIS based analysis. The result showed that the map for suitable sites produced by the GIS based analysis was reasonable from a spatial aspect, but due to the lack of groundwater seepage information, the most suitable sites developed are not necessarily the optimal choices in practice. With the aid of both the spatial analysis in GIS and seepage simulation, this two-step analysis approach provides a reliable solution to identify suitable sites for implementing MAR. This approach provides a much better reference to the study of suitable sites and possible impacts of implementing MAR in an aquifer in similar areas with water stress.