Abstract: Effective tools of controlling algae bloom by hydraulic regulation are still in lack in the Three Gorges Reservoir Area. In view of this, a 3D eutrophication model based on EFDC (Environmental Fluid Dynamics Code) eutrophication module was built using the meteorological, hydrological and water quality data of 2010 and 2011 in Dachang section and Daning River estuary. Measured data of Shuanglong and Longmen sections were employed for model calibration and validation. Results show the water temperature modeling works best with the simulated and observed values highly consistent and error statistics small (relative error smaller than 10%). Moreover, the simulated and observed values of total nitrogen and total phosphorus are well consistent, nevertheless with some deviations: the relative error of total nitrogen is smaller than 40%, and the maximum relative error of total phosphorus is 67.002%. There are large deviations in chlorophyll-a simulation, but the trends of chlorophyll-a variation could still be well reflected. This model provides technical support for controlling algae bloom by hydraulic scheduling.