Drinking water sources in many African countries have been progressively degraded over the past decades. This degradation due to human activities leads to the proliferation of algae, especially toxin-producing cyanobacteria. The presence of toxigenic algae in water has adverse consequences on human and animal health. This study aimed to determine the diversity and density of Cyanobacteria and Desmids and to identify toxin-producing cyanobacteria and environmental variables that influenced the structure of these groups of microalgae in the Loumbila reservoir in Burkina Faso located in the western part of Africa. Algal samples were collected and physico-chemical parameters were measured. Plankton species were observed under a light microscope and identified using standard methods. Species density was determined by cell counting using a Fuchs-Rosenthal chamber. Kruskal Wallis and Pearson correlation tests were performed using R software. A canonical analysis was performed using CANOCO software. In total, 205 algal species were inventoried, of which 83 species composed of 37 species of Cyanobacteria and 46 species of Desmids were identified. Microcystis aeruginosa, Staurodesmus convergens and Cosmarium connatum var africanum had the highest presence index respectively (100%, 83.333% and 77.77%). Among cyanobacteria species, toxin-producing species (30 species) and microcystin-producing species (28 species) had the highest number. In terms of species density, Microcystis aeruginosa was the most abundant species. The density of toxin-producing cyanobacteria was positively correlated (p

Desmids, Diversity, Microcystis aeruginosa, Toxin Production