Multidimensional hydrodynamic modelling becomes tricky when lacking the bathymetric data representing the continuous underwater riverbed surface. Light detection and ranging (LiDAR)-based and radar-based digital elevation models (DEMs) are often used to build the high-accuracy floodplain topography, while in most cases the submerged riverbed could not be detected because both radar and LiDAR operate at wavelengths that cannot penetrate the water. Data from other sources is therefore required to establish the riverbed topography. The inundated river channel is often surveyed with an echo sounder to obtain discrete cross-section data. In this context, an improved algorithm based on the classic flow-oriented coordinates transformation is proposed to generate the riverbed topography using surveyed cross-sections. The dimensionless channel width (DCW) processing method is developed within the algorithm to largely increase the prediction accuracy, especially for the meandering reaches. The generated riverbed topography can be merged with the floodplain DEM to create an integrated DEM for 2D and 3D hydrodynamic simulations. Two case studies are carried out: a benchmark test in the Baxter River, United States, with carefully surveyed channel–floodplain topographic data to validate the algorithm, and a 3D hydrodynamic modelling-based application in Three Gorges Reservoir (TGR) area, China. Results from the benchmark case demonstrate very good consistency between the created topography and the surveyed data with root mean square error (RMSE) = 0.17 m and the interpolation accuracy was increased by 55% compared to the traditional method without DCW processing. 3D hydrodynamic modelling results match the observed field data well, indicating that the generated DEM of the TGR area was good enough not only to predict water depths along the tributary, but also to allow the hydrodynamic model to capture the typical features of the complex density currents caused by both the topography of the tributary estuary and the operation rules of TGR.