<p>In arid and semi-arid regions, protecting groundwater from pollution is essential for public health and sustainable resource management. This study presents a multidisciplinary assessment of shallow aquifer quality, integrating isotopic tracing, statistical analysis, and metal speciation modelling. Eighteen groundwater and surface water samples were analyzed to identify geochemical processes, trace element speciation, and pollution sources. Results from hydrochemical and isotopic analyses indicate that groundwater composition is primarily influenced by water–rock interactions and recharge from the Recent Nile system, with limited recharge from old Nile channels. In addition to some anthropogenic impacts from industrial effluents and agricultural runoff impacts on groundwater quality. Saturation index modeling using PHREEQC revealed oversaturation with carbonate minerals and undersaturation with evaporitic phases. Chemical speciation of trace elements was determined; as it have a direct effect on their mobility and potential toxicity to living organism. Speciation analysis demonstrated that trace element toxicity varies by chemical form; free ionic species such as Cu²⁺ and Co²⁺ are more bioavailable and pose greater health risks than their complexed counterparts. Groundwater samples contained both aqueous and particulate species, forming complexes with ligands including Cl⁻, OH⁻, SO₄²⁻, F⁻, and HCO₃⁻. Un-complexed forms of Ba, Mn, Sr, Zn, Co, and Cu were present as free ions, indicating potential for sorption onto aquifer materials. This natural attenuation may limit mobility under low acidity and low organic matter conditions. However, it may not fully mitigate health risks, and artificial treatment could be required depending on contaminant concentrations and exposure scenarios.</p> Graphical abstract <p></p>