Vegetation colonizing fluvial sandbars provides many noteworthy functions in river and floodplain systems, but it also influences hydrodynamic processes, mainly during flooding events. Numerical modelling is generally used to evaluate the impact of floods, but its reliability is very much connected with the accuracy of the bed and bank roughness, which is eventually altered by the presence of vegetation and its height. However, for the sake of simplicity, most models tend to ignore how the sandbar roughness varies over space and time, as a function of the local vegetation dynamics (spatial distribution and height). To determine the long-term dynamic vegetation condition using remote sensing multispectral indexes, this study leverages a deep-learning method to establish a relationship between vegetation height (h), a critical parameter for vegetation roughness estimation, and vegetation indexes (VIs) collected by an uncrewed aerial vehicle (UAV). A field campaign was performed in October 2024 covering the Baishazhou sandbar, located along a straight section of the Wuhan reach of the Changjiang River Basin, China. The results show that the R² and RMSE between the real and predicted vegetation height by the trained Fully Connected Neural Network (FCNN) are 0.85, 1.10 m, and the relative error reaches a maximum of 17.2%, meaning that the trained FCNN model performs rather well. Despite being tested on a single case study, the workflow presented here demonstrates the opportunity to use UAVs for depicting vegetation characteristics such as height over large areas, eventually using them to inform numerical models that consider sandbar roughness.