The dissimilar ecological behavior of species including, extent of mobility and feeding strategies, may predispose them to greater toxic effects. This hypothesis was tested by histological-based assessment of gills and liver of pelagic (Tilapia zilli) and benthic (Clarias gariepinus and Neochanna diversus) fish species of River Owan. The fish species were sampled monthly across seasons from river sites where they were observed to be most abundant. The pathologies were examined from light micrographs, and severity was evaluated by semi-quantitative analyses. Gill pathology of Tilapiazilli showed a moderate occurrence of shortened secondary lamellae, compared with Clarias gariepinus and Neochanna diversus which showed a high incidence of very distinct structural disruptions including epithelial lifting, collapsed secondary lamella structure due to pilaster disruption. Although hepatocellular damage, fibrotic biliary disruptions and parasite incidence were the most evident pathological features in liver of all species, parasite variety and lesion severity differed across species. Principal component analysis (PCA) associated benthic species with more severe gills and liver pathologies, indicating that, benthic species in the Owan riverscape were more at risks compared to pelagic species. As such, we successfully demonstrate that relative ecological risks and potential adverse health effects on fish species could be dependent on ecological behavior and preferences. Conservation efforts particularly for endangered species could be better developed if relative risks and vulnerability of species are understood. Copyright © 2019 Elsevier Ltd. All rights reserved.