Wastewater irrigation can introduce toxic metals into the agricultural soils that may accumulate in edible plant parts. This research aimed to assess the inflows and outflows of cadmium (Cd) and zinc (Zn) in soils under a wheat-sorghum cropping system at both a control and an exposed site over two cropping seasons (2019-2020 and 2020-2021). The exposed site was irrigated with canal water contaminated with industrial and municipal wastewaters, whereas the control site was irrigated with underground water. Dry matter yields were higher at the exposed site, due to wastewater irrigation (about 9% higher in wheat and about 15-20% higher in sorghum) compared to the control site. At both sites, the primary inflow pathways were irrigation water and atmospheric wet deposition, while the major outflow pathway was crop removal. At the exposed site, net balances of both Cd and Zn were positive, ranging from + 66 to + 86 g ha-1 for Cd and from + 148 to + 301 g ha-1 for Zn. In contrast, at the control site, the Zn balance was negative, ranging from - 67 to - 228 g ha-1, whereas the Cd balance was positive, ranging from + 4 to + 7 g Cd ha-1. The concentrations of Cd and Zn in plant samples were also higher at the exposed site than at the control site. Consequently, wheat grown at the exposed site had near-desirable levels of Zn in grains (35-36 mg kg-1) whereas the Cd concentration (0.30-0.33 mg kg-1) exceeded the permissible limit of FAO. Ideally, contaminated wastewater should not be discharged into irrigation water sources. Furthermore, the choice of cropping systems and rotations for contaminated sites should consider the potential rates of metal inflows through various pathways and desired rates of outflows via crop removals. Conversely, for minimally exposed sites, Zn application to low-Zn calcareous soils remains imperative for achieving optimal crop yields.