In the last few decades, groundwater has been the main water supply to the Nuweiba alluvial fan. However, currently, the main water supply is a desalination plant. The desalination plant might be vulnerable to malfunctions resulting in a severe drought. In addition, the aquifer type in the fan is coastal. Hence, replenishing the groundwater is necessary on a long-term basis to overcome drought events in the case of emergency. To replenish the groundwater using flash-flood water, a Managed Aquifer Recharge (MAR) system could be installed. This study applies the Geo-Information System–Multi-Criteria Decision Analysis (GIS-MCDA) method to delineate the feasible locations for installing a MAR system. To delineate the feasible MAR sites via a potential map, four steps were performed: problem definition, constraint mapping, suitability mapping, and sensitivity analysis. The results show that nearly 52% of the study area is suitable for installing MAR. Additionally, around 6% of the study area shows high potential for installing MAR, whereas nearly 20% falls under the moderate potential class. The potential map shows that the high-potential MAR sites are located at the western portion of the study area, near the ephemeral stream outlet. The map could be utilized as a tool for decision-makers to plan a future sustainable development strategy.