The Guadalupe Valley Basin (GVB) in Baja California, Mexico, faces severe groundwater depletion from intensive agriculture, over-extraction, and declining precipitation. The water imbalance has been progressive, and an annual deficit of approximately 18 Mm3 was reported in 2024. In response, we identified suitable sites for Managed Aquifer Recharge (MAR) through an integrated geospatial and hydrogeological analysis. We combined aquifer data with surface datasets in a Spatial Multi-Criteria Decision Analysis (SMCDA) framework using the Analytical Hierarchy Process (AHP). The basin was stratified into two zones (valley aquifer and highlands) to account for differing recharge conditions. Sensitivity analysis and validation with observed groundwater level changes were performed to ensure model robustness. Three zones were identified as highly suitable for MAR: the central Calafia area, the Porvenir Wells area, and an upstream highland sub-basin. Areas within the 99th percentile of suitability covered approximately 0.62 km2 in the aquifer region and 1.75 km2 in the highlands. The analysis also identified areas prone to waterlogging, which may limit the feasibility of MAR projects. Our results provide a basis for guiding MAR implementation in this water-stressed basin and offer an applicable framework for similar semi-arid regions worldwide.