An investigation was made to study the variations of the environmental factors and the composition of plankton when Microcystis bloomed in Shennong River which is the primary tributary of Three Gorges Reservoir during June and August in 2008. The results show that Microcystis aeruginosa is the absolutely dominant species forming the algal bloom. The Microcystis bloom lasted about 50 d and covered about 0.2 km². The biomass of Microcystis are in direct correlation with the total phosphorus. With Three Gorges Dam stored water, the flow velocity of Shennong River has been slowed down greatly and the self-purification ability of the river declined. As a result, nutrient accumulated constantly and causing the water eutrophication. High content of nutrients in the water of Shennong River is the main reason responsible for the algal bloom formation while suitable natural conditions also contribute to the process. Based on the research, we proposed several strategies to mitigate the eutrophication and control algal blooms in Shennong River including pollution control and river ecosystom management.