Chelonians are considered good bioindicators of environmental quality. The assessment of the health status of chelonian populations in the Amazon is important because they are traditionally consumed in large numbers in riverine communities and sustainable use reserves. The present study aimed to evaluate the health of Podocnemis unifilis (Testudines, Podocnemididae) in an environmental protection area in the Amazon region in Brazil. We analyzed the biomarkers lipoperoxidation, carbonylation of proteins, occurrence of micronuclei and erythrocytic nuclear abnormalities, quantified metallothioneins, and evaluated mercury bioaccumulation. We generated pioneering data regarding biomarkers in wild Amazonian freshwater turtles. All biomarker responses did not vary significantly between the sexes. The occurrence of oxidative and genotoxic damage, as well as concentrations of metallothioneins was low compared to other studies. In addition, the bioaccumulation of mercury in the muscle of the animals was below the limit recommended for human consumption by the World Health Organization. Our results provide baseline data on mercury bioaccumulation and biomarker responses that can be useful for future comparisons with other freshwater turtles. The data also provide evidence that the sustainable exploitation of these turtles in the study area (Piagaçu-Purus Sustainable Development Reserve) does not pose a risk to local riverine communities, as the detected mercury concentrations are safe for human consumption. In this sense, our results highlight the importance of protected areas for the conservation of healthy turtle populations, at the same time ensuring the health of the human populations that use them as a food resource.