<p>This study assesses the vulnerability of the Quaternary aquifer in Qena Governorate, Upper Egypt, using a GIS-based Land Use–Intrinsic Vulnerability (LU–IV) model and compares the spatial outputs with field chemistry measurements from 38 boreholes (November 2022). The intrinsic vulnerability (IV) was mapped based on lithology, depth to water table, and slope, and integrated with land‑use data to derive an LU–IV map. Model performance was validated using nitrate (NO₃) and supported by concentrations of potentially toxic elements (PTEs) in the studied wells. Statistical analyses were performed to examine relationships between vulnerability classes and measured contaminants. The intrinsic vulnerability map classified 0.7% of the area as negligible, 22.7% as low, 52.8% as moderate, and 23.8% as highly vulnerable. Incorporating land-use factors significantly reshaped vulnerability patterns, with the LU–IV model identifying 49.7%, 24%, 4.3%, and 22% of the area as negligible, low, high, and extreme vulnerability, respectively. The significant positive correlation (r = 0.81) between LU–IV classes and NO₃, used as a vulnerability tracer, demonstrates the model’s effectiveness. This study provides the first validated application of the LU–IV model in Qena Governorate, showing that incorporating land-use information substantially improves predictions of groundwater vulnerability. The resulting vulnerability maps serve as robust decision-support tools for groundwater protection, sustainable land-use planning, and environmental management in arid and developing regions.</p>