We conducted a series of laboratory experiments to investigate the impact of vegetation on bedload transport rates depending on submergence. In the experiments, we used aluminum rods to simulate rigid vegetation, with vegetation submergence ratios (i.e., the ratio of water depth to vegetation height) ranging from 1 to 2. The bedload transport rates were measured by collecting sediment at the end of the vegetated area. The findings indicate that, with a constant bulk-averaged flow velocity, bedload transport rates decrease as the submergence ratio increases. This decrease is attributed to changes in the flow velocity distribution resulting from the flow resistance exerted by submerged vegetation. Indeed, water flows more easily through the top of the vegetation, and concurrently water velocity decreases significantly in the bottom region occupied by the vegetation. Building upon the phenomenological theory of turbulence, we propose a hydraulic radius-based method for estimating bed shear stress by incorporating the submergence ratio effect. This model enables the application of Cheng’s (2002) bedload formula, originally developed for bare beds, to predict bedload transport rates in both emergent and submerged vegetated flows. The present model, calibrated with a single parameter from experimental data, exhibited an average relative error of about 400% when validated with using experimental data (275 data in all) from our study and the relevant literature.