The pollution by metals and metalloids represents a significant environmental threat, due to the adverse repercussions they can have on aquatic organisms and on the health of human populations. Aquatic reptiles can be used as bioindicators of the presence of contaminants in watercourses. In the present study, water, carapace and blood samples from Trachemys dorbigni tortoises were collected in rural and urbanized areas, in order to identify the presence and consequences of exposure to metal(loid)s. The elements Al, As, Cd, Cr, Cu, Fe, Hg, Mn, Ni, Pb and Zn were measured in water, blood and carapace, and erythrocitary changes were also analyzed by flow cytometry and micronucleus evaluation. In the assessment of water in the urban area, the metals evaluated exceeded all established national parameters, while in the rural area, only Cd, Hg and Ni were elevated. In the carapace evaluation, the samples collected in the urban area showed higher levels of all measured metals, when compared to animals from the rural area. In blood samples only Al, Cr, Ni and Zn showed higher values in this area. Animals from the urban area also showed a higher incidence of necrotic cells, a greater number of micronucleated cells and a high rate of DNA fragmentation, resulting in cytotoxic, genotoxic and mutagenic damage. The results highlight the importance of using bioindicators to measure metallic contaminants in urban watercourses, thus estimating their impacts on the health of animals and humans, in the short and long term.