Industrial wastewater irrigation of agriculture crops could cause a lot of environmental and health problems in developing countries due to heavy metals deposition in agriculture soils as well as edible plants consumption by human beings. Therefore, this study was conducted to find out heavy metals’ concentration in industrial wastewater and soil irrigated with that wastewater. In addition, the impact of industrial wastewater irrigation on Parthenium hysterophorus and Zea mays genes involved in growth improvement and inhibition of selected plants. For this purpose, plant samples from agriculture fields irrigated with wastewater from Hattar Industrial Estate (HIE) of Haripur, Pakistan and control plants from non-contaminated soil irrigated with tape water were collected after fifteen and forty-five days of germination. Heavy metals concentration in the collected plant samples, wastewater and soil were determined and results revealed that the study area was predominantly contaminated with Cr, Pb, Ni, Cu, Co, Zn and Cd concentrations of 38.98, 21.14, 46.01, 155.73, 12.50, 68.50 and Cd 7.01 mg/kg, respectively. The concentrations of these heavy metal have surpassed permissible limit of these metals in normal agriculture soil. Expansins and cystatin (plant growth enhancers), metacaspases (plant growth inhibitor) genes expression were studied through reverse transcription polymerase chain reaction and results showed that the expression of these genes was higher in samples collected from wastewater-irrigated soils as compared to control. More expression of these genes was observed in 45 days old samples as compared to 15 days old samples and control. Taken together, this study suggests the use of Parthenium and maize for phytoremediation, however, they should not be used for eating purposes if irrigated with industrial wastewater.