This paper is based on the principles of two-medium photogrammetry, with the purpose to perform a bathymetric survey of a reef in the South China Sea, using aerial imagery acquired by UAV. The first objectives are to introduce the basic principles of two-medium photogrammetry, discuss the technical requirements of this methodology to determine an accurate refractive index of sea water, and propose a new method to calculate seawater refraction and calculate corrected reef elevations. The second objective is to analyse and integrate the elevation and depth datum for both the land mass and the undersea reef. The final objective of this paper is performing stereoscopic mensuration on the UAV photography in order to transform reef elevation and depth datum. Our test shows that aerial two-medium photogrammetry is feasible in practical application, but requires relatively high aerial photography conditions.