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Twenty-two sites were monitored in the Lower Sassandra River Basin (Côte d'Ivoire, West Africa) to examine patterns in fish species assemblage structure along environmental gradients. Hierarchical clustering of the species presence-absence data identified four types of assemblages corresponding to the man-made Lake Buyo, the main channel, and the two major tributaries. Canonical Correspondence Analysis (CCA) indicated that canopy closure, leaves-wood, aquatic plants, temperature, width, total dissolved solids and depth were the environmental factors most strongly correlated with variation in the fish assemblages. Five species: Papyrocranus afer, Micralestes elongatus, Parailia pellucida, Tilapia busumana and T. mariae were reported from the basin for the first time. The investigation of the variation in species richness led to the assessment of a major anthropogenic disturbance induced by a palm oil factory. In conjunction with the fact that the Sassandra River hosts an endemic species, Synodontis koensis, it was concluded that this basin is of high conservation priority.