Xiaojiang River, the tributary of the Three Gorges Reservoir, has suffered from eutrophication since the impoundment in 2003. Previous study showed that the lower river velocity and longer residence time are the key factors which promote the phytoplankton spring bloom. A two dimensional hydraulic and eutrophication model was developed to investigate the hydraulic and eutrophication dynamics in Xiaojiang branch. The model describes cycling of three nutrients element, namely carbon, nitrogen and phosphorus, in phytoplankton, detritus and inorganic nutrient. The effect of the hydraulic regulating of the sub-reservoir on dominance of the spring bloom was examined numerically. Artificial flood-impulse from the sub-reservoir is arranged to promote the physical disturbance in downstream river. The model predicts that flushing with water from the sub-reservoir will suppress phytoplankton blooms to some extent when the flushing water quantity is sufficiently increased. The effective suppressing river reach is the upper reaches of Gaoyang. While in the reach below Gaoyang, there is no obvious response of the phytoplankton growth to the hydraulic regulating. The eco-operation of the upstream reservoir can be used as one of the emergency alternative management for controlling the algal bloom in Three Gorges Reservoir. In order to control algal blooms in the tributary, nutrient loading should be reduced significantly.