There have already a lot of research results about the influences of the Three Gorges Reservoir on water environment in backwaters in the mainstream of the Yangtze River, but environmental impact assessment work about tributaries in the backwater area is not sufficient. Since eutrophication has occurred in many reservoirs in China, much attention should be paid to the issue that whether there will be eutriphication in the backwaters of tributaries after water storage in the Three Gorges Reservoir.Firstly, this paper estimates changes of hydraulic parameters (such as water depth, flow velocity, water surface area and water volume stored) in tributary backwaters before and after normal operation of the Three Gorges Reservoir in 2009 and predicts pollution load level (TN and TP) in 2010. And then by using Box Model,it analyses the Three Gorges Reservoir's influences on eutrophication in tributary backwaters of the Yangtze River in Chongqing section. The results show that, with average water depth of 15m in backwaters tributaries,there should be no eutrophication problem on the whole. However, it is possible for water near the bank along the reservoir with water depth under 1 meter to have the eutrophication problem in partial.A water body will subject to eutrophication of moderate level to higher level if TP concentration ranges between 0.05 mg/L and 0.11 mg/L according to standard of eutrophication indicators of Institute of National Public Hazards of Japan. Because TP concentration in backwaters of some tributaries of the Three Gorges Reservoir will certainly exceed 0.05 mg/L, we can also conclude that although there will be no higher level of eutrophication in tributary backwaters, there will be moderate eutrophication.