Nowadays, irrigation uses large amount of marginal wastewater due to continuous decline in fresh water supply. As a consequence, using this wastewater for different purposes can cause some adverse environmental impacts. Anthropogenic activities such as septic tanks, sewage ponds, and polluted drains have large influence on deterioration of shallow groundwater aquifers. So, construction of many wastewater treatment plants in these areas is mandatory to control and mitigate this deterioration. Groundwater vulnerability assessment maps and contamination simulation in unsaturated zone can be beneficial in understanding contaminants pathways and groundwater quality evolution. This work is mainly focused on aquifer vulnerability assessment to pollution and the role of vadose zone in attenuation of contaminants transport through it prior to groundwater seepage. Therefore, about 56 drainage and groundwater samples were collected and analyzed for potentially toxic elements. The most vulnerable sector was determined using GOD method revealing that central parts of the study area are the most threatened zones with some scattered sporadic zone of sensitivity to pollution and this was verified through the zonation of Pb, Fe, and Mn spatial concentrations. The leakage of these elements through the unsaturated zone was further simulated using HYDRUS-1D model for the next 10-year period to determine the extent of the pollution plumes and maximum concentration of these elements that percolate to the groundwater directly. The concentration of Fe, Pb, and Mn at the end of the simulation reached low concentrations at the bottom layer of the unsaturated zone.