In order to study the changes of stagnation points in the Yangtze Estuary influenced by the Three Gorges Dam operation, 3-D hydrodynamic and sediment transport model ECOMSED was used to simulate the dynamic process of flow varying with the river discharge and tide of the Yangtze Estuary. The results show that the location of stagnation points varied markedly in different areas after the impoundment of the Three Gorges Dam, with the large extent of downward movement during flood periods due to the hydrodynamic enhancement of the Yangtze River in the North Branch, while the movement range was smaller in the South Branch. Along with the runoff changes, the variation extent from big to small is North Channel, South Passage and North Passage, while the rank order changed as South Passage, North Channel and North Passage as valued by the tidal changes. After the impoundment of the Three Gorges Dam, the movement range of stagnation points reduced because of the reduction in river discharge. Thus, it can be considered that the turbidity maximum zone has a decreasing trend which might lead to changes in geomorphic features of the Yangtze Estuary.