Evaluating water level changes at intertidal zones is complicated because of dynamic tidal inundation. However, water level changes during different tidal phases could be evaluated using a digital surface model (DSM) captured by unmanned aerial vehicle (UAV) with higher vertical accuracy provided by a Global Navigation Satellite System (GNSS). Image acquisition using a multirotor UAV and vertical data collection from GNSS survey were conducted at Kilim River, Langkawi Island, Kedah, Malaysia during two different tidal phases, at high and low tides. Using the Structure from Motion (SFM) algorithm, a DSM and orthomosaics were produced as the main sources of data analysis. GNSS provided horizontal and vertical geo-referencing for both the DSM and orthomosaics during post-processing after field observation at the study area. The DSM vertical accuracy against the tidal data from a tide gauge was about 12.6 cm (0.126 m) for high tide and 34.5 cm (0.345 m) for low tide. Hence, the vertical accuracy of the DSM height is still within a tolerance of ±0.5 m (with GNSS positioning data). These results open new opportunities to explore more validation methods for water level changes using various aerial platforms besides Light Detection and Ranging (LiDAR) and tidal data in the future.