Muna reservoir is located in 4°32’27“N, 74°14’59” W adjacent to the municipality of Sibate, Cundinamarca, its waters come from Bogota river containing decaying organic matter, agricultural wastes and pesticides which have high pollution generated favored eutrophication processes, proliferation of insects and microalgae. Thus, as phytoremediation as part of bioremediation emerges as a solution to clean mixed water, reducing the risk of contamination of rivers and streams. Therefore, identification of microalgal biodiversity reservoir in order to estimate potential microalgae for bioremediation processes was performed. This was carried out by optical microscopy, using taxonomic keys and where the culture media, Zarrouk, Basal Bold and f/2 Guillard allowed reproduction microalgal biodiversity contained in the samples. Similarly, physicochemical parameters such as pH, dissolved oxygen, turbidity and conductivity were in-situ measured. Oscillatoria and Nostoc cyanobacteria, green algae as Scenedesmus, Eudorina, Closterium and Tabellaria diatoms, genres that have qualities phytoremediation were identified; otherwise, it was found that at temperatures above 20°C, the growth of cyanobacteria and the presence of oxygen and carbon limit in the development of these micro-algae in the reservoir is encouraged.