The photosynthetic high rate algal systems are characterized by improved growth in biomass and leachate treatment capacity. Microalgae involved in these systems are used for bioremediation of pollutants and can also indicate changes in the aquatic system by displaying variations in the structure, function and growth of communities. This study aimed to appraise the structure and dynamics of the community of microalgae associated with a high rate algal system used in bioremediation landfill leachate of San Pedro, Valle del Cauca, Colombia. Biological sample sand measuring physical and chemical parameters were taken during three phases of treatment between November 2012 and July 2013. Shannon and Simpson indices were used to assess the diversity of the system. A total of 28 especies were recorded, with Chilomonas insignis and Euglena sp. 1 as the most abundant. The study revealed variations in abundance and species composition during all phases of the system development. The first phase was dominated by Cryptophyta and the second and third phases were dominated by Euglenophyta. The dominance of organisms was associated with organics and nutrients concentration in the water. The indices showed a low diversity (between 0 and 2) due to high levels of eutrophication, the second phase was the moment of greatest diversity (H' = 1.77). Finally, knowledge of the structure and dynamics of phytoplankton is the key to maintenance and performance of this system.