The acquisition of the three-dimensional (3D) morphology of the complete tufa dam system is of great significance for analyzing the formation and development of a pellucid tufa lake in a fluvial tufa valley. The dam system is usually composed of the dams partially exposed above-water and the ones totally submerged underwater. This situation makes it difficult to directly obtain the real 3D scene of the dam system solely using an existing measurement technique. In recent years, unmanned aerial vehicle (UAV) digital photogrammetry has been increasingly used to acquire high-precision 3D models of various earth surface scenes. In this study, taking Wolong Lake and its neighborhood in Jiuzhaigou Valley, China as the study site, we employed a fixed-wing UAV equipped with a consumer-level digital camera to capture the overlapping images, and produced the initial Digital Surface Model (DSM) of the dam system. The refraction correction was applied to retrieving the underwater Digital Elevation Model (DEM) of the submerged dam or dam part, and the ground interpolation was adopted to eliminate vegetation obstruction to obtain the DEM of the dam parts above-water. Based on the complete 3D model of the dam system, the elevation profiles along the centerlines of Wolong Lake were derived, and the dimension data of those tufa dams on the section lines were accurately measured. In combination of local hydrodynamics, the implication of the morphological characteristics for analyzing the formation and development of the tufa dam system was also explored.