This study investigates the prediction of bedload transport within natural vegetation canopies, comparing it with rigid cylinder arrays. Vegetated channels exhibit more complex bedload transport due to vegetation drag and turbulence. Previous methods using rigid cylinders neglect plant morphology, leading to significant prediction errors. This study measured bedload transport in natural canopies of P. australis, A. calamus, and T. latifolia, and compared it with rigid cylinder arrays. The primary factor driving bedload transport in natural canopies is near-bed turbulent kinetic energy (TKE), which includes both bed-generated and vegetation-generated turbulence. A method was proposed to predict near-bed TKE in natural canopies. For the same solid volume fraction, transport rates in natural canopies are greater than or equal to those in rigid cylinder arrays, depending on plant shape. This indicates that plant morphology significantly affects transport rates in vegetated regions. Four classical bedload transport equations were modified to account for near-bed TKE. The Meyer-Peter-Müller equation showed the highest accuracy in predicting transport rates in vegetated landscapes. Aquatic vegetation plays a crucial ecological role in wetlands, but wetlands are under threat due to sediment loss and erosion. Wetland restoration projects aim to mitigate degradation by transporting sediment into eroded areas. Accurate predictions of sediment transport are essential for estimating sediment retention and landscape evolution. Traditional equations based on bed shear stress may not be suitable for vegetated regions. This study focuses on how to accurately assess transport rates in vegetated regions. The study highlights the importance of considering plant morphology in predicting bedload transport in vegetated channels.This study investigates the prediction of bedload transport within natural vegetation canopies, comparing it with rigid cylinder arrays. Vegetated channels exhibit more complex bedload transport due to vegetation drag and turbulence. Previous methods using rigid cylinders neglect plant morphology, leading to significant prediction errors. This study measured bedload transport in natural canopies of P. australis, A. calamus, and T. latifolia, and compared it with rigid cylinder arrays. The primary factor driving bedload transport in natural canopies is near-bed turbulent kinetic energy (TKE), which includes both bed-generated and vegetation-generated turbulence. A method was proposed to predict near-bed TKE in natural canopies. For the same solid volume fraction, transport rates in natural canopies are greater than or equal to those in rigid cylinder arrays, depending on plant shape. This indicates that plant morphology significantly affects transport rates in vegetated regions. Four classical bedload transport equations were modified to account for near-bed TKE. The Meyer-Peter-Müller equation showed the highest accuracy in predicting transport rates in vegetated landscapes. Aquatic vegetation plays a crucial ecological role in wetlands, but wetlands are under threat due to sediment loss and erosion. Wetland restoration projects aim to mitigate degradation by transporting sediment into eroded areas. Accurate predictions of sediment transport are essential for estimating sediment retention and landscape evolution. Traditional equations based on bed shear stress may not be suitable for vegetated regions. This study focuses on how to accurately assess transport rates in vegetated regions. The study highlights the importance of considering plant morphology in predicting bedload transport in vegetated channels.