The contamination of surface waters by different pollutants is an important problem worldwide. In this study, the histopathological effects of water pollution were investigated on freshwater fish species Capoeta capoeta caught from the Karasu River. Fish were caught at three different sites in the Karasu River, namely, Aşkale, Dumlu, and Serçeme. The histological changes in gill and liver of fish were detected microscopically and evaluated with quantitative analyses. In addition, heavy metals have also been determined in surface water samples from these sites. Results showed that the Aşkale site was polluted by different kinds of heavy metals. In Aşkale site, some heavy metals such as Cd, Al, As, Pb, and Mn levels were mostly detected at concentrations above than the accepted values by the Turkish Standards Institute. The presence of gill and liver histological alterations were assessed by the degree of tissue change (DTC). In gill filaments, hypertrophy and hyperplasia of the gill epithelium, lamellar epithelial lifting, lamellae shortening, vasodilatation, lamellar disorganization, blood congestion, fusion, and aneurysm were observed. In the liver, the changes included an increase in the number and size of melanomacrophage aggregates, nonhomogenous parenchyma, proliferation of the hepatopancreas, sinusoidal dilatation, vacuolization, hypertrophy of the hepatocytes, congestion and degeneration of central vein, blood congestion, pyknotic nucleus, focal necrosis, and hepatic granuloma. The histological lesions were comparatively most severe in liver. The DTC means were varied from slight to moderate of gill and moderate to severe of liver tissue in the Aşkale site, thus the site is considered to be of low quality. Some pathological alterations were observed in the Serçeme site, although their distribution was lower than sites Dumlu and especially Aşkale. The least DTC means of the Serçeme site demonstrated their good environmental quality. The results suggest that there is a close relationship between amounts of pathological alterations and environmental contamination. © 2014 Wiley Periodicals, Inc. Environ Toxicol 30: 904–917, 2015.