Wastewater production is a serious problem in Egypt, which increases as the population grows and the demand on fresh water increases. The lack of water used in agriculture in arid and semi-arid regions is being an important reason to use wastewater in agriculture. In this research, a wastewater stabilization ponds (WSPs) system with a design flow of 40000 m3/day in El-Qusiyyah city located in Upper Egypt is evaluated to make sure that the effluent from this system is inconformity with Egyptian and Food and Agriculture Organization of the United Nations (FAO) quality standards for wastewater reuse in agriculture. Monthly samples were collected from the inlet, anaerobic ponds, facultative ponds, and maturation ponds. Some physicochemical parameters as pH, biochemical oxygen demand (BOD), and total suspended solids (TSS) were measured. In addition, levels of some heavy metals were taken into consideration. Concentrations of copper (Cu), chromium (Cr), and zinc (Zn) were measured. Results showed a moderate efficiency of the system and the effluent did not match the recommended characteristics to be reused in agricultural purposes. Increasing in pH, and TSS values above the permissible limits prevent the agricultural reuse of the effluent from El-Qusiyyah wastewater treatment plant.