Concentration of heavy metals in aquatic animals mainly occurs due to industrial contamination. In this study, the concentrations of four heavy metals (cadmium, lead, mercury, and arsenic) in organs of two cyprinid fish and in water collected from three sections of the Kor River, Iran were determined using the inductively coupled plasma method. Pathological and hormonal changes due to metal contamination were also measured. The concentrations of heavy metals in tissue of fish from the middle sampling zone were significantly higher (p < 0.05) than those from the other two sampling zones, whereas no significant differences (p > 0.05) were detected between the two sexes and species. High levels of metals were found in the ovaries and testes; estradiol in females and progesterone and testosterone in males from the middle study site were significantly (p < 0.05) lower than values from the other two sites. Pathological changes in blood cells, liver, and kidneys of fishes were significantly higher in highly polluted areas (middle sampling zone). These results show that industrial activities have polluted the river and that the maximum concentrations of Cd, Pb, and Hg were higher than the permissible levels for human consumption.