The physical and biological structure of riparian vegetation fundamentally influences floodplain roughness, and thus the flood velocity and flood levels of a river. The study aims to provide detailed spatial data on the vegetation density of a floodplain, and to model the effect of the actual vegetation and various scenarios on flow conditions. LiDAR data were applied to evaluate the density and roughness of the submerged understory vegetation over the densely vegetated floodplain of Lower Tisza, Hungary. Then, HEC–RAS 2D modelling was applied to analyse the effect of the actual vegetation on flow conditions. Further scenarios were also created to predict the effect of (i) invasive plant control, (ii) no maintenance, and (iii) riparian vegetation restoration (meadows). According to the results, since the 19th Century, the increased vegetation density is responsible for a 17-cm flood level increase, and if the vegetation grows even denser, a further 7 cm could be expected. As the vegetation density increases, the overbank flow velocity decreases, and the crevasses and flood conveyance zones gradually lose their function. Simultaneously, the flow velocity increases in the channel (from 1 m/s to 1.4 m/s), resulting in an incision. Applying LiDAR-based 2D flow modelling makes it possible to plan sustainable riparian vegetation maintenance (e.g., forestry, invasive species clearance) from both ecology and flood control perspectives.