The Sabzkooh river, one of the Karoon branches that is 50 kms long, is located in Chaharmahal and Bakhtiari province, south west part of Iran. At this time there are a few active fish farms on this river and they are continuing to grow in numbers and in size. There are many demands to licence receiption and construction continually. In this study at the range of 30 kms along the river from Chahartagh to Roodarood, water quality of the river is evaluated in cause of physiochemical parameters, poisons, heavey metals, microbiological factors. The effects of fish farms constructions on morphology and flow regime of the river is also studied. The conclusions show that the water quality of the river is decreasing from up to down stream. Undecomposed organic material, heavey metals in fish foods, chemical material to antisepticise of the ponds and the drugs to control the pathogene factors are the most important pollutants of the Sabzkooh river. Immethodical and non standard constructions of fish farm ponds caused to much sensibility of river to turbulence, so much sediment production, lateral erosion increasing and decreasing the effect of vegetation on river stability. On the other hand 70 percent of the study range of this river is in insufficient morphological situation.