Tufa barrages play an important role in fluviatile tufa ecosystems and sedimentary records. Quantifying the height of tufa barrage is significant for understanding the evolution and development of the Holocene tufa barrage systems. However, for submerged tufa barrages, there is no low-cost non-contact method to retrieve barrage height. Generally, it is difficult to recognize small tufa barrages by means of remotely sensed satellite data, but the combination of unmanned aerial vehicles (UAV) and Structure-from-Motion (SfM) photogrammetry makes it possible. In this study, we used a fixed-wing UAV and a consumer-grade camera to acquire images of the submerged tufa barrage in Lying Dragon Lake, Jiuzhaigou National Nature Reserve, China, and estimated the height of the tufa barrage through UAV-based photogrammetric bathymetry. On this foundation, the relationship between barrage height and its spectrum was established through band ratio analysis using UAV-derived geometric bathymetry and digital orthoimages, which provided an alternative strategy to characterize the height of submerged tufa barrages. However, the spectral characteristics of submerged tufa barrages will oscillate with changes in the environmental conditions. In future research, we will consider using a dedicated aquatic multispectral camera to improve the experimentation.