Histological and ultrastructural analyses of gills were observed in Nile tilapia collected from three different waterbodies in southeast Brazil: an urban lake in a park in the city of São Paulo, a reservoir in a rural city, and a commercial aquaculture facility. These waterbodies were analyzed and classified as hypereutrophic, eutrophic, and supereutrophic, respectively, with 310.00, 94.00, 28.00 of phosphate ( μg L−1) and 65.49, 24.95, 12.83 of chlorophyll (μg L−1). A significant difference in the histological alterations index (HAI) was observed only in fish from the urban lake, with the presence of cell hypertrophy, hyperplasia, aneurism, and other alterations. When compared to the other groups, a large quantity of rodlet cells was also observed in the urban group. These results demonstrate the correlation of eutrophic states of water with gill morphology. Also discussed is the premise that large amounts of organic material dissolved in water can alter the morphology of the fish gills.