An existing system of natural waste stabilization ponds (WSPs) in El-Qusiyyah city, Upper Egypt was monitored through one year to evaluate the fate of heavy metals and nutrients included in wastewater. The plant treats domestic wastewater with design daily flow rate of 40,000 m^3 and stills hydraulically under-loaded. It comprises two parallel lines each consists of anaerobic, facultative, and four maturation ponds in series. Variations of some physicochemical parameters (T,pH,DO,〖BOD〗_5,and TSS) along the ponds system were observed and evaluated. Evaporated water from ponds and its impacts were assessed. Concentration changes of four heavy metal ions (〖Al〗^(3+),〖Zn〗^(2+),〖Cr〗^(6+),and 〖Cu〗^(2+)) and various forms of nutrients (nitrogen and phosphorous) along the treatment line were observed. The treatment plant was found to be working well regarding to the investigated physicochemical parameters. General decrease in heavy metals and nutrients concentration along the wastewater stream in the plant was observed. The overall removal efficiency for 〖Al〗^(3+),〖Zn〗^(2+),〖Cr〗^(6+),and 〖Cu〗^(2+) was found to be 80.62%, 69.69%, 72.99%, and 71.53%, respectively. The system showed moderate overall removal efficiencies for total nitrogen and phosphorous as 68.56% and 39.37%, respectively. Based on national and international standards, the results of heavy metals and nutrients out of the treatment plant showed the effluent suitability for agricultural irrigation regarding to the studied parameters.