This study evaluates groundwater quality in the Wadi Feiran Basin, Southwestern Sinai, by integrating hydrochemical analysis, pollution assessment, and human health risk assessment (HHRA) with morphometric characterization of surface runoff. Morphometric analysis shows that sub-basins vary in runoff potential, reflecting differences in size and topography. Groundwater quality exhibits significant variability, with pH, electrical conductivity, total dissolved solids, and total hardness exceeding World Health Organization (WHO) limits in several samples. Hydrochemical facies analysis indicates that silicate weathering, evaporite dissolution, ion exchange, saline intrusion, and anthropogenic contamination are the dominant processes shaping groundwater chemistry. Pollution assessment using Nemerov’s Pollution Index identifies nitrate and iron as key contaminants, with nitrate exceeding WHO standards in nearly half of the samples. HHRA reveals substantial non-carcinogenic risks, particularly for children, due to elevated nitrate levels, while long-term exposure also suggests potential carcinogenic effects. Overall, 60% of the sampled groundwater is unsuitable for drinking, underscoring the urgent need for monitoring and management strategies to protect public health and ensure sustainable groundwater use in the basin.