Gill anomalies in two fish species (Geophagus brasiliensis and Astyanax bimaculatus) were compared among three freshwater systems with different water quality: one eutrophic river, one eutrophic reservoir, and one oligotrophic reservoir. The raised hypotheses are that reservoirs with low water quality (eutrophic) have fish with more gills anomalies compared with reservoirs with high water quality (oligotrophic), and that the more stable environmental conditions of eutrophic rivers have fish with better healthy conditions than eutrophic reservoirs that have lesser stable environmental conditions. Gills of 36 adult individuals of G. brasiliensis and 23 of A. bimaculatus collected during the winter 2008 and winter 2009 were examined, and the proportions of occurrence of nine histological alterations were compared for the two species among the three systems using a binomial t test for independent samples. Histological changes in fish gills that are reversible and unspecific, such as epithelial lifting, interstitial edema, leukocyte infiltration, hyperplasia of the epithelial cells, lamellar fusion, and vasodilatation were common in both fish species in the three systems. However, lamellar aneurism, which is a more serious and often irreversible anomaly, and lamellar blood congestion occurred only in fish from the two reservoirs. Alternatively, necrosis occurred more in fish from the river. Fish gill anomalies in both species did not differ between the two reservoirs, despite having different water quality. We rejected the hypothesis that reservoirs with lower water quality have fish with more gill injuries compared with high water quality reservoirs. Moreover, the eutrophic river seems to affect differently the healthy condition of fish species, compared with the eutrophic reservoir.