The present study aimed at evaluating the environment quality of the Santa Cruz Channel estuary (area 1) and Sirinhaém river estuary (area 2), Northeastern Brazil, using histopathological biomarkers of liver and gills of fish species with different trophic levels as indicators. It was collected liver and gills from five species: Bairdiella ronchus (n=24) and Gobionellus stomatus (n=34) in the area 1; Caranx latus (n=35), Centropomus undecimalis (n=24) and Centropomus parallelus (n=29) from area 2. The liver showed several damages, such as, hepatic steatosis, necrosis, vacuolar degeneration, and infiltration. Centropomus undecimalis had the highest Histopathological Index of Liver (HIL). Gills exhibited moderate to severe alterations for all species, such as the lifting of epithelial cells, lamellar aneurysm, and rupture of the lamellar epithelium. Centropomus undecimalis in area 2 and G. stomatus in area 1 had the higher number of alterations in their organs. Both areas have been historically affected by mercury (Hg) pollution in área 1 and by the sugarcane industry in area 2 and the species used as biomarkers has been proven to be severely damaged in both estuaries. Species chosen in this study were considered good bioindicators of pollution and the combination of biomarkers methodologies in two organs, pioneering in the Northeastern of Brazil, was efficient in diagnosing the health status of the area using fish as bioindicator.