The purpose of this study was to evaluate histopathological changes in gills, spleen, liver, kidney and intestine of farmed rainbow trout in four different stations along with Barm Spring (Lordegan, Iran). In this study, at least 15 fish from each farm were captured and following autopsy, sampling was carried out from the gills, liver, spleen and intestine of fish. After tissue sectioning, samples were stained with hematoxylin and eosin. Tissues were studied with a 400X magnification. Gill lamella stick together, gill hyperplasia, exfoliation of gill epithelium, epithelial necrosis and hypertrophy and swelling of gill lamellae, hypertrophy and liver fat degeneration, glomerular and collecting duct of urine degeneration, increase in the lumen space, shrinking the glomerular as well as an increase in melanomacrophage centers (MMC), disorganization of ellipsoids in the spleen, necrosis of epithelial cells, exfoliation of the mucous layer of intestine were the major histopathological alterations observed in the fourth (less than 20% of the group) and the third (a few of fish) group. The results of this study showed that these alterations may be due to an increase in the chemicals in downstream water. Therefore, these histopathological changes could be used as an appropriate biomarker to water quality monitoring.