We propose a novel technique to measure the small-scale three-dimensional features of a shallow-water coral reef using a small drone equipped with a consumer grade camera, a handheld GPS and structure from motion (SfM) algorithms. We used a GoPro HERO4 with a modified lens mounted on a DJI Phantom 2 drone (maximum total takeoff weight < 2 kg) to perform a 10 min flight and collect 306 aerial images with an overlap equal or greater than 90%. We mapped an area of 8380 m2 , obtaining as output an orthorectified aerial photomosaic and a bathymetric digital elevation model (DEM) with a resolution of 0.78 and 1.56 cm pixel-1, respectively. Through comparison with airborne LiDAR data for the same area, we verified that the location of the ortho-rectified aerial photomosaic is accurate within ~1.4 m. The bathymetric difference between our DEM and the LiDAR dataset is -0.016 ± 0.45 m (1s). Our results show that it is possible, in conditions of calm waters, low winds and minimal sun glint, to deploy consumer-grade drones as a relatively low-cost and rapid survey technique to produce multispectral and bathymetric data on shallow-water coral reefs. We discuss the utility of such data to monitor temporal changes in topographic complexity of reefs and associated biological processes.