Abstract Digital Elevation Models (DEMs) are used to derive information from the morphology of a land. The topographic attributes obtained from the DEM data allow the construction of watershed delineation useful for predicting the behavior of systems and for studying hydrological processes. Imagery acquired from Unmanned Aerial Vehicles (UAVs) and 3D photogrammetry techniques offer cost-effective advantages over other remote sensing methods such as LIDAR or RADAR. In particular, a high spatial resolution for measuring the terrain microtopography. In this work, we propose a Structure from Motion (SfM) pipeline using UAVs for generating high-resolution, high-quality DEMs for developing a rainfall-runoff model to study flood areas. SfM is a computer vision technique that simultaneously estimates the 3D coordinates of a scene and the pose of a camera that moves around it. The result is a 3D point cloud which we process to obtain a georeference model from the GPS information of the camera and ground control points. The pipeline is based on open source software OpenSfM and OpenDroneMap. Encouraging experimental results on a test land show that the produced DEMs meet the metrological requirements for developing a surface-runoff model.