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Anthropogenic and climatic factors are important determinants of algal distribution in aquatic systems. This study aimed to identify temporary pond-groups of phytoplankton assemblages and to establish the interactions between environmental variables and phytoplankton structure. Phytoplankton samples were collected and preserved with 5% formalin; water samples for chemical analysis were taken in August and September 2007, 2008, and 2009 in 86 ponds randomly selected in the Sahelian sector and the Sudanian sector (protected and unprotected areas) of Burkina Faso. Plankton species were examined using light microscopy and identified using standard methods. A Fuchs-Rosenthal chamber was used for algal cell counting. NMDS ordination, indicator species analysis and canonical analysis were performed using Pc-Ord and CANOCO. Kruskal-Wallis and Mann-Whitney U-tests using the software Statistica were performed to compare parameters between pond-groups. Three pond-groups were identified: the Sahelian pond-group, dominated by Lyngbya martensiana and Pseudanabaena constricta; the protected area pond-group, dominated by Euglena caudata and Trachelomonas raciborskii; and the unprotected area pond-group, dominated by Closterium venus and Euglena proxima. At P < 0.05, species composition and abundance in algal groups were mostly associated with nitrate, pH, dissolved oxygen, and conductivity. The Sahelian and the Sudanian sectors were different in pH, water transparency, and species richness. Univariate and multivariate analyses illustrate that variations in the physicochemical properties of water and algal structure followed climatic and anthropogenic gradients. The classification of ponds into algal associations demonstrated that algal assemblages may be used as reliable indicators of habitat conditions., (© 2019 Phycological Society of America.)