Abstract: The geological environment in estuarine delta region is fragile and sensitive to natural and anthropological changes, and the evolution of alluvial siltation in delta port is influenced by engineering structures. Dongying Port in the Yellow River Delta is dominated by silty sands and active sediment transport. The key issue of engineering in such an area is the change of sea bed flushing and siltation caused by engineering structure. By applying the digital elevation model (DEM) of underwater topography constructed by the measured bathymetry data since the construction of Dongying Port in combination of numerical hydrodynamic simulation, the evolution of the siltation process and engineering impact of Dongying Port were explored. Results show that, due to the change of seafloor topography caused by waves and tides, the situation of siltation in the near-shore area of Dongying Port has evolved from single erosion to near-shore erosion and offshore siltation. The engineering structure affected the local tidal flow velocity and direction, and a high-speed cross-current with a maximum velocity of 0.7 m/s appeared at the mouth gate, which led to a scour pit with a diameter of about 1 km at the head of the north breakwater. The sheltered area of the engineering structure had a siltation-promoting effect, and the size of the sheltered area was related to the tidal flow direction and the angle between the engineering structure and the shoreline. However, under the action of waves and residual currents, more than 0.5 m erosion still existed in the sheltered area from 2007 to 2015. The persistent erosion has increased the instability of sea breakwaters and seawalls. Therefore, it is urgent to strengthen the detection and protection of the port.