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Digital elevation model (DEM) has been frequently used for the reduction and management of flood risk. Various classification methods have been developed to extract DEM from point clouds. However, the accuracy and computational efficiency need to be improved. The objectives of this study were as follows: (1) to determine the suitability of a new method to produce DEM from unmanned aerial vehicle (UAV) and light detection and ranging (LiDAR) data, using a raw point cloud classification and ground point filtering based on deep learning and neural networks (NN); (2) to test the convenience of rebalancing datasets for point cloud classification; (3) to evaluate the effect of the land cover class on the algorithm performance and the elevation accuracy; and (4) to assess the usability of the LiDAR and UAV structure from motion (SfM) DEM in flood risk mapping. In this paper, a new method of raw point cloud classification and ground point filtering based on deep learning using NN is proposed and tested on LiDAR and UAV data. The NN was trained on approximately 6 million points from which local and global geometric features and intensity data were extracted. Pixel-by-pixel accuracy assessment and visual inspection confirmed that filtering point clouds based on deep learning using NN is an appropriate technique for ground classification and producing DEM, as for the test and validation areas, both ground and non-ground classes achieved high recall (>0.70) and high precision values (>0.85), which showed that the two classes were well handled by the model. The type of method used for balancing the original dataset did not have a significant influence in the algorithm accuracy, and it was suggested not to use any of them unless the distribution of the generated and real data set will remain the same. Furthermore, the comparisons between true data and LiDAR and a UAV structure from motion (UAV SfM) point clouds were analyzed, as well as the derived DEM. The root mean square error (RMSE) and the mean average error (MAE) of the DEM were 0.25 m and 0.05 m, respectively, for LiDAR data, and 0.59 m and –0.28 m, respectively, for UAV data. For all land cover classes, the UAV DEM overestimated the elevation, whereas the LIDAR DEM underestimated it. The accuracy was not significantly different in the LiDAR DEM for the different vegetation classes, while for the UAV DEM, the RMSE increased with the height of the vegetation class. The comparison of the inundation areas derived from true LiDAR and UAV data for different water levels showed that in all cases, the largest differences were obtained for the lowest water level tested, while they performed best for very high water levels. Overall, the approach presented in this work produced DEM from LiDAR and UAV data with the required accuracy for flood mapping according to European Flood Directive standards. Although LiDAR is the recommended technology for point cloud acquisition, a suitable alternative is also UAV SfM in hilly areas. © 2019 by the authors. Licensee MDPI, Basel, Switzerland.