The fish gill is in direct and standing contact with the immediate external environment and, therefore, is highly vulnerable to aquatic pollutants. In this study, Prochilodus argenteus were caught at two different points in São Francisco river. The first point is located near Três Marias dam, while the second is placed downstream the Abaeté river. Chemical approaches showed the presence of metals contamination in the first point. Thus, the main goal of this study was to investigate the possible toxic effects of these contaminants and the likely use of biomarkers on fish gills. Biometric data of length and weight of fish were obtained in order to calculate the condition factor as an organismal biomarker. The histological changes in gills and alterations in mucous and rodlet cells occurrence were detected microscopically and evaluated with quantitative analyses. Myeloperoxidase (MPO) and Eosinophil Peroxidase (EPO) were also assessed in fish gill. The analysis of the water and sediment samples revealed the presence of metals at the two points. As and Cd were detected at higher concentrations at point 1. The presence of lamellar cell hyperplasia, lamellar fusion, lamellar oedema and inflammatory foci varied according to the point. Additionally, mucous and rodlet cells and MPO and EPO activities showed variability according to the environmental conditions. Furthermore, with exception of lamellar hyperplasia and eosinophil peroxidase activity, all others parameters showed sex-variation responses. At the first point, male fish showed a chronical inflammation in gills due to the lowest activity of MPO and EPO, as well as low occurrence of inflammatory foci and glycoprotein secretion by mucous cells, while female fish presented an opposite pattern of response to the same environmental conditions. Therefore, we suggest the use of such biomarkers in future monitoring of aquatic systems, taking into account the sex-variation responses.