In Nablus Governorate, agrifood industries including dairies, olive mills, and slaughterhouses discharge diverse wastewater streams without pretreatment due to the lack of onsite pre-treatment systems. Nablus West Sewage Treatment Plant (NWSTP) is facing major operational challenges with associated economic and environmental impacts. NWSTP is not designed to co-treat high organic pollution loads of industrial origin without pretreatment. Treated waste water from NWSTP, the main water flow in Wadi Zomer, is mixed downstream with raw industrial discharges from Nablus West. Besides impairing Wadi Zomer water quality, the illicit industrial discharges into public sewer networks lead to non-compliance of NWSTP with the Palestinian Specification (PS 227, 2010) pertaining to industrial wastewater discharge into water bodies. This study investigates the role of natural wetlands along Wadi Zomer in reducing the organic and inorganic pollution loads from diverse industrial discharges including the residual pollution loads originating from the NWSTP. Along a length of 5 km downstream of NWSTP, four sampling stations were selected to assess the purification capacity of Wadi Zomer including the role of natural wetlands plant (Phragmites australis) in pollution loads reduction. Since, the watercourse of Wadi Zomer and its major tributaries pass through various hydrogeological, topographic landscape with diverse industrial sites, four main sampling stations (S1 to S4), distributed over a flow distance of 5 km long from NWSTP (S1), and were chosen for water quality monitoring. A total number of one hundred samples (44 water, 44 sediment and 12 vegetation samples) including one vegetation control, were analyzed for physical and chemical parameters over a period of eight months (August-December, 2019, and Jan-March, 2020). The results show that sampling stations S2 (0+0.5 km) and S3 (0+3.0 km) were identified as key stations reflecting an increase in pollution loads due to illicit industrial discharge and sewer overflow discharge form NWST during emergency conditions in the results obtained. The BOD values varied significantly along sampling sites and ranged from 6.64 to 437.10 mg/l. The study revealed that the water in S1 and S2 had BOD levels below PVL standard (PSI, 227/2010) and that S3 and S4 had BOD levels (437.1±300.8), (333.9±233.7) mg/l respectively, above the maximum permissible limits. Similar fluctuation tendencies in the concentration of COD and nutrients (NH4 and PO4). Compared to control site values, the water samples from all sites (S1-S4) showed a decreasing tendency in the concentrations of heavy metals (Fe>Cu>Zn>Cr >Ni) and were below the national standard limits. The pollution tendency of heavy metals in the sediment followed the same decrease pattern in water samples with the flow course of Wadi Zomer. The concentration of Fe (6687 mg/kg) and Cu (1384.7 mg/kg) were found at highest in sediment samples (S1-S4), this might be due to point, and non-point sources of pollution, with a similar tendency, found for Zn, Cr and Ni for all sites. This may be due to direct discharge of industrial wastewater from metal, tanneries, and textile industries, established in the western side of Nablus city, into Wadi Zomer without pretreatment. Wadi Zomer catchment area is coupled to the mountain aquifer, where polluted environmental flows could infiltrate into the aquifer. Significant phytoremediation capacity was found for iron, copper and zinc within the roots of P. australis, and largely retained in the sediment. Despite the short-term period of data collection, the findings in this study should still provide technical help and a valuable reference for policymakers and joint service councils to implement effective pollution control and monitoring associated with science-based land-use planning. Further study is required to examine the seasonal variations in mass balance for water and metal contents in the different compartments of the natural wetland system along the Wadi Zomer course. The results obtained suggest the development of rehabilitation programs using nature-based technologies along Wadi Zomer watercourse and help selection of primary monitoring stations aiming at sustainable water management for the whole watershed area. The urgent needs to improve the environmental flows of the Wadi watercourse considering the multi-beneficial uses for agricultural irrigation and recreational use warrant further investigations.