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This study used the levels of pollutants and the histopathological analysis of the gonads and liver of Sarotherodon melanotheron sampled in Lake Nokoué and Lake Toho, both in Benin (West Africa) to assess the health status of the ecosystems. Sixty adults (30 males and 30 females) of this species were caught during the flooding seasons from both Lake Nokoué, and Lake Toho (as a reference). The physicochemical parameters of the water and the heavy metal contents (Pb, Cd, Hg) in water/sediment/fish of three sites (S1, S2, S3) in Lake Nokoué and two sites (S4, S5) in Lake Toho were analysed. Results confirm very strong organic status with organic pollution index ranging from 1.25 to 1.5. Pb, Cd, and Hg levels in the water/sediment/fish muscle tissue of Lake Nokoué were far exceeding international standards. The histopathology of gonads revealed testis-ova up to 40% in males and follicular atretic oocytes up to 33.33% in females, indicated oestrogenic effects from the pollutants with a delay of spermatogenesis and stimulation of oogenesis. The histopathology of the liver revealed the presence of regressive changes. The findings call for actions to protect the ecosystem from pollution and attention in terms of health of humans consuming fish products from Lake Nokoué. [ABSTRACT FROM AUTHOR]