The seaward waterway of Jiaomen includes Zhenxiang and Longxuenan waterway. Channel dredging is the main method of the navigation training project. Based on analysis of river evolution and the 2D estuarial suspended sedimentation numerical model with the nested grids, the effects of the dredging project in Zhenxiang and Longxuenan waterway on flow dynamics and sediment transportation in Yamen estuary are studied.Main conclusions are as follows: 1) The river evolution of Zhenxiang and Longxuenan waterway is relatively steady.2) After implementation of the dredging project in Zhenxiang and Longxuenan waterway, the change of flow dynamics and sediment transportation in Yamen estuary is very small. The main changes take place vicinity of navigation channel with dredging project and its beach. 3) Due to the small amount of dredging works, there is little influence on the water-sediment condition in the seagoing area of Jiaomen eastuary.