Abstract Submerged vegetation canopies are widespread and influence bedload sediment transport in rivers, wetlands and deltas. However, the impacts of submerged canopies on sediment transport have not been fully quantified. This study used model Vallisneria denseserrulata to construct submerged flexible canopies in a mobile bed. Velocity, turbulence, and bedload transport were measured for a range of canopy submergence and density and compared with theoretical models predicting near‐bed turbulent kinetic energy (TKE) and bedload transport. Within a submerged canopy, the near‐bed TKE includes not only bed‐ and stem‐generated TKE, but also TKE generated in the shear‐layer at the canopy top. The prediction of near‐bed TKE and transport rate within submerged canopies improved when the contribution from canopy‐shear layer‐generated TKE was included. The proposed model can accurately evaluate sediment transport and thus increase the prediction accuracy of vegetated landscapes, providing guidance for the maintenance and restoration of rivers, wetlands and deltas.