Pollution of aquatic ecosystems often results in adverse environmental disturbances, including individual and/or sub-individual changes in fish. The aim of the present study was to examine possible reproductive health effects in male and female, based on a histological assessment of Clarias gariepinus sampled in Bagoue River impacted by mercury from the artisanal gold mining. Fish were collected between August 2018 and April 2019 during two seasons from four stations differently impacted. A histological assessment was done on three target fish organs (liver, ovary and testis). Water and sediment samples were analysed for total mercury (T-Hg) concentration. Histological alterations were semi-quantitatively assessed, and the results were classified according to the severity of the histological response identified. Microscopic assessment revealed alterations of the gonads and liver tissues. A higher incidence of reaction pattern (Regressive changes, Inflammation and Circulatory disturbance) was found in liver tissues than in gonads tissues (Regressive changes). T-Hg levels were higher upstream than downstream in ovaries and testis tissues. Paradoxically, the lesions observed in these organs were more pronounced downstream than those found in fish from upstream during rainy season. According to total index, the organs examined downstream suffered severe damage unlike upstream sites. Also, comparison of degree of alteration between testes and ovaries indicates a greater impact of ovarian structures especially on downstream sites. The effect of anthropogenic impact appears to be visible downstream as the concentration of chemical pollutants and exposure time determine the severity of the damage. Alterations in ovarian follicles, spermatogenic cells and liver tissues may reflect damage to the process of gametogenesis, which may reduce the reproductive capacity of individuals over the long term.