This study describes the concentrations of heavy metals and arsenic (As) and the basic histopathological changes in the internal organs of gibel carp Carassius auratus gibelio from five sites of the Amur River basin. Gibel carp from Sindinskaya Passage had the highest liver concentrations of zinc (Zn) (31.95 ± 13.443), copper (Cu) (12.52 ± 5.746), manganese (9.22 ± 8.121), and cadmium (0.37 ± 0.660 mg/kg wet weight [ww]) compared with fish captured from the Bol'shoi Ussuriiskii Island area and Kadi Lake; however, concentrations of nickel (0.22 ± 0.156 mg/kg ww) were not significantly different, and concentrations of lead (0.19 ± 0.121 mg/kg ww) were higher than those in fish from Kadi Lake. Mean concentrations of metals and As in muscles were lower than Russia's recommended limits for food products; however, concentrations of Cu, Zn, and Hg in individual fish were greater than the limit. Kidney disease was detected in 100% of sampled carp. Kidney disease was characterized by the formation of numerous granulomas in kidney tissues between the renal tubules. The degree of granulomatosis varied among sites. Granulomatous kidney disease in gibel carp is widespread in many reservoirs of the lower Amur River basin. The following histopathological changes were detected in liver: vacuolization of hepatocytes, hypertrophy of multiple hepatocytes, binuclearity, presence of numerous irregularly shaped nuclei in hepatocytes, karyopyknosis, diffuse necrosis of hepatocytes (in some cases focal), and edema. Necrotic changes in hepatocytes, which are important indices of the toxic effect of pollutants, were found in the majority of investigated carp from the lower Amur River basin. Some fish had simultaneous pathological alterations in multiple organs.