Algal blooming in 4 major rivers introduces substantial impacts to water front activity. Concentrations of algae are increasing at major points along the Geum River. Ecosystem food webs can be affected by algal blooming because blue-green algae release toxic materials. Even though there have been many studies on blue-green algae, its causality to environmental factors has not been completely determined yet. This study analyzed the exclusive correlation between various hydrometeorological, water quality, and hydrologic variables and the cell number of cyanobacteria to understand causality of blue-green algae in the Geum River. A prewhitening process was introduced to remove the autocorrelation structure and periodicity, which is useful to evaluate the effective relationship between two time series.