Abstract Aquatic vegetation plays an important role in the flow structure of open channels and thus changes the fate and the transport of sediment. This article proposes a three-dimensional turbulence model by introducing vegetation density and drag force into the control equations of water flow in the presence of vegetation. The model was used to calculate the impacts of submerged vegetation on the vertical profiles of longitudinal flow velocities, the changes of the depth-averaged flow velocities in a compound channel with emergent vegetation in the floodplain, the removal of suspended sediment from the channels by emergent vegetation, and the bed changes around and in a vegetated island. Numerical investigations show that aquatic vegetation retards flow in the vegetation zone, reduces the sediment transport capacity, and contributes to erosion on both sides of the vegetated island. Calculated results agree well with experimental results.