Most of Southern Mediterranean water courses suffer from numerous types of pollution. This study presents a comprehensive performance assessment of a pilot CW system for removing various contaminants from the Litani River, Lebanon. The physico‐chemical, pathogens and trace metal parameters were analyzed for river water as well as for the wetland effluent. Results revealed that the average removal efficiencies were 87.01% for COD, 64.99% for BOD5, 86.18% for TSS, 43.11% for NO3N, 34.82% for NH4N, 55.07% for PO4P and 73.05% for K. The removal efficiency of faecal coliforms was around 99.84%. Influent and effluent heavy metal pollution (Cu, Pb, As and Ni) concentrations greatly exceeded the range of the environmental limit values due to industrial emissions in river water. CWs seem to be a promising green technology for Lebanon for the reduction of bacterial contamination. Further studies are required to improve treatment modules for different pollutants, including metals.