The Suzhou Creek Sluice is currently the largest underwater plain gate in the world, with a single span of 100 m. It is located in a tidal estuary at the junction of the Huangpu River and Suzhou Creek in Shanghai, China. In this study, physical and 2D vertical mathematical models were used to investigate and distinguish the mechanism of siltation downstream of an underwater plain gate from that of other gates types. According to quantitative data obtained by site investigation and the application of the physical hydrodynamic models, it was found that the characteristics of the tidal estuary as well as the fact that the sluice span is equal to the creek width are the major reasons contributing to siltation. A possible desiltation treatment system is proposed for the underwater plain gate. The system includes selection of a suitable location that allows the determination of a reasonable top elevation of the sluice floor, reserving sufficient space under the gate to accommodate siltation, setting up a mechanical desiltation system, and flushing silt along with overflow over the top of the gate. Furthermore, on-site hydraulic silt flushing experiments and a topography survey were conducted. These results showed that the measurement system is effective, and by maintaining this scheduled operation once a month, the downstream riverbed has been maintained in a good condition.