Guribu catfish (Sciades herzbergii) is a resident species in estuaries of Maranhão, Brazil. The aim of this work was to determine the feasibility of integrated analysis of the branchial lesions and gonadosomatic index of Sciades herzbergii in order to evaluate the effects of pollutants in São Marcos' Bay. The first site (S1) is located near the Ilha dos Caranguejos and was used as a reference area for being an environmental protection area. The second site (S2) is located near the ALUMAR/ALCOA port, and was used as a potentially polluted area. Fish were collected at each site, forty-eight in S1 and forty in S2. Gills were fixed in 10% formalin, and usual histological techniques were used in the first right gill arch, with inclusion in paraffin and sections of 5 µm thickness. There were no histopathological changes in animals captured at the reference site. However, in those catfish collected in the potentially contaminated area it was observed several branchial lesions, such as lifting of the lamellar epithelium, fusion of some secondary lamellae, hypertrophy of epithelial cells and lamellar aneurysm. The analysis using the gonadosomatic index (GSI) showed significant differences, being higher in fish analyzed from the reference area (P < 0.05). The branchial lesions and GSI were sensitive for monitoring environmental impacts of different locations at São Marcos' Bay, Maranhão, Brazil.