Drones are an ecological tool used increasingly in shark research over the past decade. Due to their high-resolution camera and GPS systems, they have been used to estimate the sizes of animals using drone-based photogrammetry. Previous studies have used drone altitude to measure the target size accuracy of objects at the surface; however, target depth and its interaction with altitude have not been studied. We used DJI Mavic 3 video (3960 × 2160 pixel) and images (5280 × 3960 pixel) to measure an autonomous underwater vehicle of known size traveling at six progressively deeper depths to assess how sizing accuracy from a drone at 10 m to 80 m altitude is affected. Drone altitudes below 40 m and target depths below 2 m led to an underestimation of size of 76%. We provide evidence that accounting for the drone’s altitude and the target depth can significantly increase accuracy to 5% underestimation or less. Methods described in this study can be used to measure free-swimming, submerged shark size with accuracy that rivals hand-measuring methods.