The objectives of this study were to construct a three-dimensional water quality model (EFDC) for the river reach between Chilgok Weir (CGW) and Gangjeong-Goryong Weir (GGW) located in Nakdong River, and evaluate the effect of hydraulic controls, such as water level and flow rate, and phosphate loading reduction on the water quality and algae biomass. As a result of model cailbration (year 2017) and validation (year 2018), the model accurately simulated the temporal changes of the upper and lower water temperatures that collected every 10 minutes, and vertical distribution of water temperature. The temporal variations of observed dissolved oxygen, organic matter, nitrogen and phosphorus species were properly simulated. Seasonal fluctuations of algae biomass by group were adequately reproduced. However, the deviations between measured and simulated values were significant in some period, possibly due to the uncertainties of the parameters associated with algae metabolism and the lack of zooplankton predation function in the simulations. As a result of scenario simulations to control the water level and flow rate, the thermal stratification was resolved as the water level was lowered and the flow rate increased. The flow velocity at which the water temperature stratification was resolved was about 0.1 m/s, which is consistent with the previous study results of Baekjae Weir in Geum River. As a result of scenario simulation of running the water level of GGW from EL. 19.44 m to EL. 14.90 m (4.54 m drop), Chl-a and algae cell density decreased significantly. In particular, depth averaged cyanobacteria, which causes algal bloom, declined by 51.4% (year 2017) and 46.4% (year 2018) in the low water level scenario compared to the existing management level. Simulations of the flow double incremental scenario (2Q) showed that Chl-a decreased by 2.8% (year 2017) and 8.7% (year 2018), as well as the cell density of diatoms and green algae. The cell density of cyanobacteria increased, however, because the high concentrations of cyanobacteria in the upstream boundary conditions directly affected downstream due to increased flow velocity. In the scenario of reducing the typical inflow phosphate load to 50% (IP3), Chl-a decreased by 20.9% (year 2017) and 13.6% (year 2018). The seasonal algae reduction and limiting factor fluctuations of the IP3 scenario showed that the effect of phosphorus load reduction on algae control is greatest in May-June, when temperatures are high and flow rates are scarce. The results of this study are in agreement with the previous studies that maintenance of critical flow velocity is effective for controlling cyanobacteria, and suggest that the upstream algae concentration and phosphorus load reduction should be considered simultaneously with hydraulic control to prevent algal overgrowth of Gangjeong-Goryong Weir.