This study aimed to explain how the changes in certain hydrological, meteorological and physicochemical factors influence the cell density of the cyanobacteria Microcystis aeruginosa in the Nakdong River. Occurrence patterns of M. aeruginosa were analyzed between 1993 and 2010 (N =96) using a self-organizing map. The cell density of M. aeruginosa was sensitive to certain meteorological, hydrological and physicochemical factors. In addition, our clustering analysis results identified specific limnological features under different environmental conditions. Cluster 1 suggested that high rainfall and increased river flow, dam discharge, total phosphorous and phosphate concentrations were associated with low M. aeruginosa cell density (June–July; monsoon season). However, cluster 2 suggested low irradiance since water temperature decreases with irradiation time, and thus low M. aeruginosa cell density (April–June and after November). Finally, cluster 3 was indicative of high water temperature and irradiance, increased irradiation time, low phosphate and nitrate concentrations, and high M. aeruginosa cell density (August, after the monsoon season). Taken together, these results suggest that rainfall, river flow, water temperature and nutrient concentration (i.e. , phosphates and nitrates) were the primary factors that affected cyanobacterial bloom occurrence in the Nakdong River. M. aeruginosa blooms can be suppressed by employing an integrated water resource management program that accommodates meteo-hydrological factors along with the effective control of exogenous nutrient sources.