Agricultural irrigation using wastewater containing heavy metals (HM) might impose risks in bioaccumulation in foods. The current study was performed to assess the status of HM in terms of water-soil−plant systems in Kandahar, Afghanistan, where industrial and domestic wastewater was partially reused for irrigation. Water, soil, and plant samples were collected from wastewater sites in Haji-Arab (HA), Bala-Karz (BKZ), and Mahal-e-Nejat (MN) in comparison with those from a freshwater-irrigated site in Char-Bagh (CB). The HM levels in unfiltered water samples remained lower than the World Health Organization (WHO) and Food and Agriculture Organization (FAO) permissible values, but the HM concentrations in soil and crops were higher at the HA, BKZ, and MN (wastewater-irrigated sites) than those at the CB site (freshwater-irrigated site). Lead (Pb) levels were high in soils (43−83 mg/kg) and crops (18−36 mg/kg) and extremely exceeded the safe limits even for those crop samples cultivated in the freshwater-irrigated site. Continuous wastewater irrigation increased the HM concentration in water, soil, and plants, but the Pb pollution was found to be ascribed to the minerals in that area since the underground water was showing high Pb levels. The bioaccumulation of HM in the studied sites was related to the cultivated crops and correlated with the land use in the watershed area. This study is important in understanding the risks associated with HM and exercising prudence when applying various irrigation resources in Afghanistan.