The wastewater from the Razi petrochemical complex contains high levels of salts and heavy metals. In the present research, the effects of different wastewater dilution levels (0, 25%, 50%, and 100%) were studied on two wheat cultivars—Chamran and Behrang. The wastewater contained high levels of NH4+, NO3-, PO43-, and SO42-, and Mg, Ca, K, Na, Cu, Zn, Fe, M, and Ni. The toxic levels of mineral elements in the wastewater resulted in a significant decline in the K, P, Si, and Zn content of leaves. Irrigation with the wastewater resulted in a significant reduction in photosynthetic characteristics including chlorophyll fluorescence (Fv/Fm and PIABS), intercellular CO2, net photosynthesis, water use efficiency, and photosynthetic pigments. The reduction in photosynthesis was followed by a significant decrease in the carbohydrate content and, subsequently, plant height, leaf area, and grain yield. Increasing the wastewater concentration reduced leaf thickness and root diameter, accounting for the decrease in xylem and phloem vessels, the root cortical parenchyma, and mesophyll thickness. The bulliform cell size increased under wastewater treatment, which may suggest induction of a defense system against water loss through leaf rolling. Based on the observed negative effect of wastewater on physiology, morphology, anatomy, and yield of two wheat cultivars, reusing wastewater with high levels of total suspended solids and salts for irrigation cannot be approved for wheat crops.