The main goal of this study was to examine the use of cyanobacteria for evaluating the quality of running water. Accordingly epilithic cyanobacterial communities were collected in Dez River and Ojeyreb drain in south of Iran. Samples were collected in two seasons: autumn and spring. Effective physical and chemical factors on the structure of cyanobacterial communities and the dispersion of the species in relation with them were determined using PCA and CCA analyses. The Shannon-wiener biodiversity index was used to define the species diversity. The concentration of Nitrate as main nutrient had significant increase in Drain stations. A decline in species richness was observed associated with these increases in nutrient load in both seasons in different cyanobacterial community structure. The results indicated that order Oscillatoriales had higher proportion of cyanobacteria species at Drain. The species Oscillatoria chlorina, Chroococcus minor, Phormidium tenue and Lyngbya kuetzingii S had the most positive correlation with nutrient factor. Species Lyngbya infixa and Lyngbya mesotrichia had the most negative correlation with nitrate. Our results confirm the using of cyanobacteria species as indicators for monitoring eutrophication in rivers and define them as water eutrophication bioindicators.