The performance of an existing system of waste stabilization ponds (WSP) in Upper Egypt is evaluated. The sewage treatment plant was commissioned in April 2002 and it is still extremely underloaded hydraulically and organically. The plant receives an average domestic flow of 10583 m3/day, which is lightly mixed with industrial wastes. The ponds system comprises three anaerobic ponds in parallel, followed by nine facultative ponds arranged in three parallel series, and three maturation ponds in a single series. Local and cumulative removal efficiencies of SS and BOD5 along the ponds system are investigated. Variations of pH value along the ponds series are studied with their effects on heavy metals removal, faecal coliform (FC) die-off, and photosynthesis activities of algae. The total amount of the daily-evaporated water from WSP is found to be 4701 m3, which represents 44.4% of the mean daily-flow entering the plant. The influence of the evaporated water from WSP on flow rates of wastewater through ponds, hydraulic retention times (HRT), the volume of effluent leaving the plant, and SS and BOD5 removal efficiencies is cleared. The system was found to be successfully producing physicochemical safe effluent to be reused for crop irrigation or discharged into surface and coastal waters, according to the European Union (EU) quality requirements. The results emphasise the tolerance of the used system at low loading without odour production, grow of rooted macrophytes, or significant loss of efficiency.