Unmanned aerial vehicle (UAV) images and structure-from-motion (SfM) methodology allow very high resolution surface reconstruction. This fairly low-cost and time-saving method is used for northern bog hydrology characterisation. The primary interest of this study lies in seasonally changing bog pool water levels. The study site is located in a potential conflict zone where water extraction from an underground oil shale mine threatens protected wetlands. The study involves two test areas that were surveyed three times, allowing spatio-temporal quantification of seasonal changes of the bog surface. Aerial lidar data and manual measurements were used to assess the quality of SfM surfaces and discrepancies between the different methods were analysed. Overall, there is a good fit between the methods used, validating the use of SfM methodology in a natural wetland environment. This study demonstrates that the nearby mine is influencing the seasonal water-level fluctuations of the protected wetland.