Water quality and the distribution of some heavy metals in three different organs of Lepomis gibbosus from the Cine Stream were studied. Also, histopathological changes in gill, liver, and muscle tissue were examined at light microscopical level. Micronucleus (MN) formation in fish erytrocytes, as an indicator of chromosomal damage, has been increasingly used to detect the genotoxic potential of environmental contaminants. The frequency of MN was examined from samples of fish from the Cine Stream and a control group. MN frequency was higher in fish samples caught from the Cine Stream than that in the control group. The chemicals ammonia, nitrite, nitrate, orthophosphate, and sulphate were determined as parameters that possibly affect the gill, liver, and muscle morphology. Zn was the most accumulated metal in tissues as well as in water. Maximum metal accumulation occurred in both liver and gills. For histopathological examinations, samples of gills, liver, and muscle tissues of L. gibbosus were studied by using light microscopy. In this study, a significant decrease in mean length of primary and secondary lamellae were observed. Moreover, cellular proliferation developed with secondary lamellae fusion, ballooning degenerations or club deformation of secondary lamellae, as well as distribution of necrotic, hyperplastic and clavate secondary lamellae. In the liver, altered staining, swollen and ruptured parenchymal cells, loss of cord structure, reduce of glycogen in hepatocytes, and vacuolar structure filled with cellular debris and many dark particles were seen. In muscle tissue, focal necrosis, cellular dissolution, and a decline or loss of striation in muscle fibres were found.