The Yeongsan River in southwestern Korea is 150 km long and has a basin area of 3,551 km². A number of hydraulic structures have been installed along the river, including an estuary dam and two weirs (Seungchon and Juksan). While these structures aid in regional water security and reduced flooding, they stagnate water flow and frequently cause algal blooms during the summer. This study simulated the algal bloom and water quality characteristics in the middle and downstream sections of the Yeongsan River under different weir and estuary dam operating conditions using the Environmental Fluid Dynamics Code-National Institute of Environment Research (EFDC-NIER) model. Results showed that when the management levels of the Juksan Weir and estuary dam were maintained, the simulated water levels were 3.7 and -1.2 m in the Juksan Weir and estuary dam sections, respectively. When both the Juksan Weir and estuary dam were open, the water levels varied with the tide and were maintained at an average of 0.2-0.6 m in contrast, when the Juksan Weir alone was open, the water level was between -1.2 and -0.9 m in line with the management level of the estuary dam. Opening the Juksan Weir alone reduced the algal blooms by 72-84% in the Juksan Weir section, and opening the estuary dam alone reduced the algal blooms by 83% in the estuary dam. This improvement was attributed to the reduced water retention time and dilution due to seawater inflows.