Nile tilapia is an exotic species produced in Brazilian aquaculture. The aim of this study was to constitute a pathological diagnosis in Oreochromis sp. with a noticeable presence in a river in southern Brazil, and to verify the origin of these fish in this natural habitat, an environment with high sanitary precariousness due to discharges of industrial effluents. A total of 30 fish were collected during three sampling events and their health status was assessed by parasitological fauna survey, parasitological indices and histopathological examination of the gills, liver, spleen and kidney. Five species of monogenea were identified infesting gills and stomach: Cichlidogyrus sclerosus, C. halli, C. thurstonae, Scutogyrus longicornis and Enterogyrus cichlidarum; and 4 species of trichodinidae infesting the body surface and gills: Trichodina magna, T. compacta, T. centrostrigeata and Paratrichodina africana. The results showed differences according to the seasonality of the collection, with higher parasite count and larger tissue alterations in summer. Histopathological analysis fluctuated from moderate to severe, but necrosis prevailed in all organs and in all fish, indicating that these fish did not enjoy full health.