The 2D numerical simulation of river flow requires a large amount of topographic data to build an accurate Digital Terrain Model which must cover the main river channel and the area likely to be flooded. DTMs for large floodplains are often generated by LiDAR flights. However, it is often impossible to obtain LiDAR data of permanently inundated river beds. These areas are often surveyed and discrete cross-sections of the river channel are obtained. This work presents an algorithm to generate the missing information for the areas between cross-sections. The algorithm allows to generate a river bed which preserves important morphological features such as meanders and thalweg trajectory. Two benchmark cases are studied: a synthetic river-floodplain system and a real case application on a reach of the Ebro river in Spain. The cases are analyzed from a geometry and hydrodynamics perspective by performing 2D simulations with good results.