Jordan, an arid to semi-arid and extremely water-scarce country, relies heavily on groundwater, rendering the Wadi Shuaib sub-basin a critical yet vulnerable resource. Contamination threats from septic-tank leakage, overflows from the Assalt and Fuhais wastewater treatment plants, and diffuse agricultural pollutants necessitated assessing and refining groundwater vulnerability via the DRASTIC index in a GIS framework. The standard DRASTIC model, utilizing seven hydrogeological parameters from hydrological, geological, soil, land-use, and well data, produced a vulnerability map classifying the 172 km² basin into five categories: very low to very high. About three-quarters of the area exhibits low to very low vulnerability, while high (6%) and very high (5%) classes concentrate in the south-western sector, driven by shallow water tables (<1.5m), permeable alluvial Entisols, and focused recharge that accelerate contaminant percolation. Validation employed a Groundwater Quality Index (GQI) for E. coli, nitrate, and turbidity against Jordanian drinking-water standards, revealing generally high GQI scores (90–99%) but post-storm deteriorations exactly in high-vulnerability zones. Sensitivity analysis (P-values <0.05, R²) highlighted the Impact of vadose zone, net recharge, hydraulic conductivity, and topography as key contaminant transport controls, warranting higher weights for these and lower weights for depth to water, soil media, and aquifer media. The optimized DRASTIC scheme enhanced alignment between vulnerability classes and GQI distributions, offering a realistic pollution risk portrayal, particularly in recharge hotspots. The resulting maps constitute a decision support tool for delineating wellhead protection areas, prioritizing monitoring, and guiding land use planning adaptable to other semi-arid basins via local calibration and water-quality validation.