This study analyzes quantitative algae mitigation, using chlorophyll-a as an indicator, through waterbody management techniques such as pulses released from upstream dams, employing a three-dimensional numerical model. Numerical simulations focused on algae reduction through dam operations by investigating nine scenarios based on Chuncheon Dam, Soyang Dam, and Uiam Dam, located in the upper and lower reaches of Uiam Reservoir of Korea. These scenarios, aligned with actual dam operation manuals, aimed to differentiate the impact of each dam’s operation by decreasing water residence time for Uiam Reservoir. The Uiam Reservoir, smaller than the upstream Chuncheon Dam and Soyang River Dam, is significantly influenced by their discharge rates. During summer, temperature differences exceeding 7 °C between discharges from Chuncheon Dam and Soyang Dam inflowed into the right side and the left side, respectively, of the reservoir, leading to poor mixing, which was further hindered by islands within the reservoir. Consequently, due to the influence of the different base water temperatures of the Bukhan River and Soyang River and the topographical characteristics, the impact range varied depending on the operation of each dam, and the amount of algae mitigation differed at each point. In emergency situations where algae blooms proliferate rapidly, appropriate dam operations in water bodies with large dams upstream and downstream, like Uiam Reservoir, can be effective in mitigating algae at specific regions of the reservoir.