In developing countries, using non-conventional water for irrigation is a traditional and cost-effective tool. However, its long-term use for agriculture and forestry will led to toxic metal bioaccumulation in plants and soil environment. Copper (Cu) is an essential plant nutrient but its excess accumulation can cause significant issues and risks to human health following food crop consumption. The present study was conducted with the aim to assess impact of copper (Cu) in the five wheat varieties (Seher-2006, Faislabad-2008, Watan, Galaxy-2013, Punjab-2011) at 7-ecological sites during the two growing seasons (2017, 2018). The source of irrigation included the ground water, industrial wastewater and sewage water. The Cu concentrations were subsequently determined via ecological environment (water, soils) and below and above ground plant organs (shoots, roots, and wheat grains) and phytostabilization potential assessment using various pollution indices. Results of this study revealed that mean Cu concentration in different wheat varieties and treatments were varied from 1.53 to 1.07–3.22 mg/kg, 0.58 and 1.94 mg/kg, 0.43–2.39 mg/kg, and 0.23–0.78 mg/kg in amended soil, root, shoot, and grains, respectively. Wheat cultivar, Seher-2006 showed highest Cu transfer from shoot to grain following irrigation with ground water while lowest after industrial water irrigation. High content of Cu was obtained in water and toxicity was higher than the maximum permissible limit. In case of grain and soil samples the copper contents were present within the safe limits. The value of all the indices for Cu were found less than 1 except for bioaccumulation factor and translocation factor that were greater than 1 for some samples. Our results revealed that the studied varieties of wheat crop were safe for consumption but the continuous usage of wastewater for irrigation may pose health risks after many years of consumption because some samples showed the high value for bioaccumulation factor and transfer factor. Wheat varieties possess desirable traits that are vital for phytoremediation purposes.