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Flood occurrence is increasing due to the expansion of urbanization and extreme weather like hurricanes; hence, research on methods of inundation monitoring and mapping has increased to reduce the severe impacts of flood disasters. This research studies and compares two methods for inundation depth estimation using UAV images and topographic data. The methods consist of three main stages: (1) extracting flooded areas and create 2D inundation polygons using deep learning; (2) reconstructing 3D water surface using the polygons and topographic data; and (3) deriving a water depth map using the 3D reconstructed water surface and a pre-flood DEM. The two methods are different at reconstructing the 3D water surface (stage 2). The first method uses structure from motion (SfM) for creating a point cloud of the area from overlapping UAV images, and the water polygons resulted from stage 1 is applied for water point cloud classification. While the second method reconstructs the water surface by intersecting the water polygons and a pre-flood DEM created using the pre-flood LiDAR data. We evaluate the proposed methods for inundation depth mapping over the Town of Princeville during a flooding event during Hurricane Matthew. The methods are compared and validated using the USGS gauge water level data acquired during the flood event. The RMSEs for water depth using the SfM method and integrated method based on deep learning and DEM were 0.34m and 0.26m, respectively.