Wetlands not only provide abundant resources for human beings, but also play an important role in ecological balance. Wetlands are abundant in the Yangtze River Estuary (CWYE). Due to the influence of vegetation in wetlands, of which the characteristics such as vegetation density are in spatial change, the hydrodynamics and sediment transport in the CWYE are complex. Therefore, three-dimensional numerical simulations in the CWYE were conducted based on Delft3D to analyze the hydro-sediment dynamics affected by vegetation. The traditional sediment module in Delft3D, which determines sediment initiation through the bottom shear stress calculated by flow velocity, was improved considering the influence of wake turbulence caused by vegetation stem on sediment suspension. Results have shown that vegetation reduced the flow velocity which decreased the turbulence, while the wake turbulence caused by vegetation stem increased it. The sediment suspension in wetlands depended on the relationship between the decrease of turbulence caused by decreasing velocity and the increase of turbulence caused by vegetation wake turbulence. The improved model in this paper can be used for hydro-sediment dynamics simulation in coastal wetlands as well as other vegetated areas. © 2024 Elsevier Ltd