In tropical region, fish communities serve as crucial markers of the health of lake habitats. Based on experimental and commercial fishing, we investigated fish community structure of three tropical reservoirs Faé, Taabo and Kossou from October 2017 to October 2018. Fish species diversity, abundance and richness were assessed, and Focused Principal Component Analysis (FPCA) was used to evaluate the relationship between the fish communities and environmental variables. A total of 51 fish species belonging to 19 families and 9 orders were identified. Cichlids were most represented family in all lakes. Taabo Lake recorded the highest number of species (45) while Faé Lake was the low diversify with 30 species. Shannon’s diversity index and equitability were highest in Kossou Lake; rarefied richness was highest in Faé Lake, while these three indices were lowest in Taabo. Enteromius macrops dominated at Taabo and Kossou lakes whereas Pellonula leonensis dominated in Faé. Similarity analyses showed that a distinct distribution of fish communities exists between Faé and Taabo lakes, Faé and Kossou lakes. However, between Taabo and Kossou lakes, composition did not change. High transparency and temperature and low conductivity greatly influenced the fish community structure.