This paper investigated the effectiveness of natural wetlands (Phragmites australis) along Wadi Zomer in reducing the organic and inorganic pollution loads from diverse industrial discharges including occasional emergency discharges from Nablus West Sewage Treatment Plant (NWSTP), Palestine. We monitored physical and chemical parameters at four selective sampling stations (S1-S4) along Wadi Zomer with a length of 5 km downstream of NWSTP to assess the purification capacity of Wadi Zomer treatment wetlands (water, sediment, and vegetation) with Phragmites australis in pollution loads reduction. The results showed that S2 (0+0.5 km) and S3 (0+3.0 km) reflected an increase in pollution loads due to illicit industrial discharge and sewer overflow discharge from NWSTP during emergency conditions. BOD values varied significantly along the sampling sites from 6.64 mg/l (S1) to 437.10 mg/l (S3). The BOD at S1 and S2 in water samples were below the Palestinian Water Standard (PWS) compared to S3 and S4 with 437.1 and 333.9 mg/l, respectively. Water samples from all sites (S1-S4) showed a decreasing tendency in heavy metals concentrations (Fe>Cu>Zn>Cr >Ni) and were below the PWS limits, sediment samples followed the same decrease pattern for Zn, Cr, and Ni content with Wadi Zomer flow course. The concentration of Fe (6687 mg/kg) and Cu (1384.7 mg/kg) were highest in the sediment samples (S1-S4); this might be due to non-point sources of pollution. The research demonstrated that phytoremediation is a sustainable nature-based technology for the restoration of heavily polluted surface water bodies in Palestine.