The objective of this study was to evaluate the levels of environmental contamination in a protected area in the Brazilian Amazon. For this, two areas were chosen along the Mearim River: the reference area (A1) and the potentially contaminated area (A2), where water samples were collected, for physicochemical and microbiological analyses, as well as specimens of Hoplias malabaricus, for the evaluation of biometric data and incidence of branchial lesions. The physicochemical analyzes of the water from both areas showed contamination (low levels of dissolved oxygen, tubidity and high iron concentrations, especially in A2). The microbiological analyzes showed that all water samples showed total coliform values higher than those acceptable by CONAMA and WHO (with higher values in A2), in addition to E. coli values higher than those allowed by legislation in A2. Regarding biometric data, male and female fishes were significantly longer and heavier in A1 during the dry and rain seasons and the gonadosomatic index also showed higher values in A1 than in A2 in both seasons. H. malabaricus showed gill lesions of minimal to moderate pathological importance in A1 and A2, indicating that specimens from both areas of the Mearim River showed biological responses to contamination. The observed changes in the water quality, bimetic parameters and the histological analyzes of the specimens of H. malabaricus directly reflect on the quality and health of the fishes in the Mearim River, and point to the urgent need for prevention and remediation of contamination in these ecosystems.