The construction and management of the waterways at the Yangtze River Estuary are facing a new situation of profound changes in the river regime and new requirements such as ecological priority.To further improve the comprehensive carrying capacity of the waterways，we analyze the main changes in the river regime of the Yangtze River Estuary in recent decades and sum up the regulation（design）ideas for the deep waterways at the estuary.The physical process of viscous fine-grained sediment movement in fresh and salt water mixing and tidal environments and the mechanism of waterway siltation at the Yangtze River Estuary are sorted out，including the stratification of salinity and sediment concentration，turbulence suppression，baroclinic effect of suspended sediment，longitudinal and cross flow sediment transport，bedload like transport of suspended sediment near the bottom of the high concentration layer，gravity flow transport of floating mud，and laminar transport of non-cohesive sediment.On this basis，we point out some noteworthy problems in the construction and maintenance of the waterways at the Yangtze River Estuary and further research directions.We also put forward suggestions for studies of the sediment budget at the open boundary of the estuary and the influence of organisms on the stability of the riverbed.The conclusions and suggestions can serve as a reference for deepening waterway regulation at the Yangtze River Estuary.