In the Republic of Bénin, aquatic ecosystems are subject to poisoning risks due to the inappropriate use of pesticides, such as washing of empty bottles in rivers and using pesticides to catch fish. In some areas, cotton fields are located near riverbanks, increasing the probability of pesticide emission to the river. To assess contamination levels in the Ouémé River catchment area, different fish species were collected from different geographical areas along the river. DDT, its metabolites and isomers were the most frequently identified pesticides in fish flesh, alpha-endosulfan, beta-endosulfan, dieldrin, telodrin, lindane and octachlorostyrene were also detected. Concentrations of pesticide residues in fish ranged from 0 to 1364 ng/g lipid. A preliminary risk assessment indicated that the daily intake of chlorinated pesticides by people consuming fish from the Ouémé River still is rather low and does not present an immediate risk.