The Shenzhen-Zhongshan sea-crossing bridge connects the cities of Shenzhen and Zhongshan, across the “three shoals and two deep troughs” in the Pearl River estuary. A lot of piers and large-scale artificial islands in the water area will have impacts on the hydrodynamic environment of the Lingdingyang estuary, the inner part of the Pearl River estuary. In this research, the physical model for the bridge is built to analyze the impacts of the project on the hydrodynamic environment of the Lingdingyang estuary. The experimental results show that: the scheme A2 has the greatest impacts on the sea level, the others take the second place; the changes in sea level and flow field are sensible near the artificial island and the main piers; the impacts of the artificial island on the hydrodanamic environment are the greatest, the impacts of the ventilation shafts, anchorage, king tower, towers located on the Lingdingyang sea area take the second place; there will be no great changes near the non-navigable bridge pier; and the the area 5,000 m away from the bridge has a tiny change. Overall, the Shenzhen-Zhongshan project has little impacts on the Lingdingyang estuary. Based on this research and other previous researches, experts have unanimously recommended that the scheme A3 (a bridge across the Lingdingyang waterway combined with the Fanshi submerged tunnel) should be taken as a reasonable and feasible scheme.