Blooming of algae has been a primary issue of concern for heavily polluted aquatic ecosystems. The chlorophyll-a (Chl-a) concentration depends on various hydrological, biochemical and anthropogenic components, which makes prediction of algal blooms complicated. A river regulation project in Yeongsan River, South Korea, involving the construction of a weir, had substantially altered the flow regime. A prewhitened time series analysis is a useful method for delineation of a causal relationship between two environmental variables. This study explores the impact of river regulation on algal blooming using both the prewhitened cross-correlation method and principal factor analysis. Both individual and comprehensive causality structures were configured for the variation in Chl-a concentration. A prewhitened cross-correlation analysis indicates that the water quality response patterns of the river system were changed to those of a reservoir after the river regulation project. A principal factor analysis of correlations indicates that the weir construction had a stronger impact on algal concentration than both the hydro-meteorological factor and difference in sampling location. Variation in stochastic structures from nutrients and water quality factors to algal bloom was substantially reduced by the construction of a weir, which can be explained by the relatively uniform flow pattern throughout the river regulation practice.