The main goal of this study is to assess the role of Algae in the treatment of wastewater and its capability to improve the performance of the free surface wetland as a green solution. It offers a non‐conventional water resource that participate in solving the water scarcity issue in Egypt. This study was carried out in Lake Manzala Water Research Station which is located at the tail end of Bahr El Baqar Drain in Northern Delta in ‏Egypt. A pilot scale wetland consisting of four parallel basins under natural climatic conditions were used for the experiment. The first cell was cultivated with Reeds (traditional plant used in wetlands), while the algae were cultivated in the three other basins. Three different microalgae and algae species (Chlorella, Spirulina and Azolla) were experimented and compared to assess for the finest removal efficiency for different contaminants as BOD, COD, TN, TP, TC, FC and heavy metals. A tailor‐made module was developed with Excel Visual Basic Application programming language to compare the efficiencies of the different treatment systems. Results showed that BOD and COD best removal results were reached by Chlorella with 88% and 84% removal efficiencies respectively. Results also showed that Azolla is the most efficient treatment media for drainage water containing high concentrations of TN while Spirulina was found to be the most efficient in extracting the heavy metals such as Aluminum (Al), Iron (Fe) and Manganese (Mn).