This paper describes the flow & sediment conditions near the site of immersed tunnel of Hong Kong-Zhuhai-Macao bridge, and analyzes the back-silting characteristics and influential factors of the test excavated trench. Using a 2D flow and sediment transport model, this paper analyzes the change of flow due to the engineering implementation and the motion of dredging ship overflowed sediment. The model results show that the flow velocity decreases 40%~60%, the overflowed sediment of 0.005 g/L isolines spread away less than 2 km and distributes at a narrow strip. The overflowed sediments deposit mainly into the trench bottom, and a small part to the side slope. Under a comprehensive consideration of the dredging overflow sediment deposition and natural sediment deposition, and combining with the formula of back-silting, we estimate that the annual average strength of sediment back-silting is 1.3 ~2.8 m/a after the trench excavation .