The primary goal of this study is to shed light on some important factors that control algal bloom in a large-scale regulated river system. Long-term impacts of environmental conditions on algal dynamics were investigated in the Paldang dam watershed, Korea. Dam inflow, water temperature, chlorophyll-a, TN, PO4-P and TP data collected at five major dams located on the North Han River (NHR) and at four water quality monitoring sites on the South Han River were analyzed for 21 years (1992 to 2012) to examine spatio-temporal variations in each. A pattern of slightly increasing chlorophyll-a and nutrient levels in the NHR since 2001 indicates that algal dynamics were affected by the increased nutrient levels as well as the reduced flow conditions (−10% to −37%). The temporal variations in monthly averaged data collected during summer monsoon seasons (mainly July) over the two decades show that high chlorophyll-a levels observed in both rivers corresponded to the relatively lower flow condition, which means a reduced amount of dam water release due to low or no rainfall over a short period of time, and abnormally high water temperature. This study shows that flow control is most critical for effectively managing algal level in the rivers in the short term, and nutrient management in the watershed is the key to reducing the potential for algal bloom in the long term.