Water pollution from human activities is largely a result of the discharge of wastewater and industrial waste into rivers. Phytoremediation, the technique that uses plants to remove pollutants from the polluted waters, is a growing field of research because of its various environmental advantages. This study aims to evaluate the efficiency of a constructed wetland in removing pollutants and treating the polluted waters of the Litani River in Lebanon, by means of two aquatic plants, Phragmites australis and Sparganium erectum. Results showed that the levels of the physicochemical and biological parameters measured on water samples at downstream of the wetland were lower than those obtained at upstream. Results revealed that average removal efficiency was 41% for chemical oxygen demand (COD), 54% for biological oxygen demand (BOD5), 97% for nitrate (NO3−), 40% for nitrite (NO2−), 67% for phosphate (PO43−), while it was negative (−62%) for sulfate (SO42−), indicating an increase in sulfate content in the treated effluent returning to the river. On the other hand, most of the effluent chemical and biological characteristics were within the provisional discharge limits of effluent to water body set by the Ministry of Environment (MoE) and Lebanese Wastewater Reuse Guidelines of the Food and Agricultural Organization of the United Nations (FAO). Statistical analyses also showed significant variations (p < 0.5) among the two sampling sites along the wetland. Our findings clearly demonstrate that phytoremediation is a viable solution to remove pollutants in a competitive environment and improve the quality of contaminated waters by acting as a sink for various contaminants. The gained experience may be scalable to other sites and environments across the country.