Water quality deterioration hinders economic and social development in developing countries that are facing freshwater security and shortages. Based on the collection of 29 water samples, this study focused on the relationship between sewage treatment plant and groundwater system surrounding it using multidisciplinary approach that combines the characterization of groundwater system and its connection with surrounding canal and drains, using chemical and isotopic characterization revealing that there is a direct relation between the surface water system and surrounding groundwater system. About 58% of the groundwater samples and all surface water samples in the investigated area are threatened by high concentrations of trace elements. The multivariate statistical analysis elucidates that anthropogenic effect and fertilizers sewage contamination are the main causes of groundwater pollution. Nearly, 31% and 11.5% of groundwater samples were posing oral chronic non-carcinogenic health risk and dermal chronic risk for adult, respectively, while all surface water samples were posing oral chronic non-carcinogenic health risk, with no dermal hazard. The uncharged species of Fe and Al are expected to be more mobile in groundwater because they would not be attracted to the surface charge of minerals. Inorganic ligands (HCO3−, SO42−, Cl−, and NO3−) act as nucleation centers that were linked with those trace elements creating new species with higher solubility degree in water that are transported away randomly for long distances in the water path.