The comprehensive mapping of groundwater contamination zones is vital for sustainable water resource management, especially in underdeveloped countries facing urban and industrial pressures. This study investigates, for the first time, the groundwater vulnerability of the Djibouti aquifer system located in the north of the East Africa Rift System (EARS). This area, which is home to 72.8 % of the country's inhabitants, has been impacted by rapid urbanization including industrial activities and the discharge of untreated wastewater. This study compares multiple groundwater vulnerability modeling frameworks, including DRASTIC (Depth to groundwater, net Recharge, Aquifer media, Soil media, Topography, Impact of the vadose zone, and hydraulic Conductivity), DRASTIC–LULC (Land Use Land Cover), DRASTIC–AHP (Analytic Hierarchy Process), AHP–DRASTIC–LULC, DRASTIC–NSGA-II (Non-dominated Sorting Genetic Algorithm-II), and NSGA-II–DRASTIC–LULC. Spatial autocorrelation analysis (Moran's I > 0.95) has been used to improve the reliability and interpretability of the vulnerability maps. Groundwater vulnerability maps indicate that high and very high vulnerability zones (13.59–47.47 % and 1.02–21.70 %, respectively) are primarily located in the eastern and northern sectors. Moderate to low vulnerability zones (30.81–56.45 %) are prevalent in the central part of the study area. Sensitivity analysis identified key parameters such as aquifer depth, vadose zone impact, and aquifer medium. The LULC factors significantly improved model sensitivity and enabled better identification of at risk zones. The NSGA-II–DRASTIC–LULC model outperformed other modified DRASTIC methods, achieving a correlation of 0.58, an AUC of 0.84, and an RMSE of 1.13. These findings may provide a critical scientific basis for Djibouti's policymakers to prioritize land-use zoning and implement targeted protection measures in the identified high-risk zones, thereby securing a sustainable water future for the region's growing population.