In this study, we investigated the correlation between the number of cyanobacterial species and the water quality factors after installation of Nakdong river weirs. Factor analyses of water quality factors were also performed. The results of correlations showed that there was no significant water quality with the cyanobacterial concentration but the correlation coefficient of nutrients increased from the upstream to the downstream. There was a significant correlation between W·T and pH as important water quality factors for the growth of cyanobacteria. In the downstream region of Nakdong river, algae were more frequently detected than in the upstream region, and the blooms of algae species seem to be influenced by the higher pH and the influx of the phosphorus from the upstream tributaries. Nutrient concentration was higher in the downstream region than in the upstream region due to the effects of tributaries Geumho river and Nam river in Nakdong river. As a result of the factor analyses, nitrogen species were the principal factors in the upper region, and phorsphorus species were the principal factors in the downstream region.