Smart unmanned aerial systems integrated with accurate Global Navigation Satellite System (GNSS) are now an important approach for acquiring spatial data and have the potential for a wide range of engineering applications. This study was endeavoured to determine the feasibility of Unmanned Aerial Vehicle (UAV) or Drone-based technology to monitor the status of water conservation structure and to examine their suitability by GIS-based Multi Criteria Decision Making (MCDM) inputs derived from High Resolution 3D Imagery (HRI). For the Pauha-Kurmigundra Narwa (PKN) Restoration, updated thematic data is used based on High-resolution Aerial orthomosaic images and Digital Surface/Terrain Model obtained through UAV survey. To compensate for the shift from the real world due to positional errors in UAV, six reference points were surveyed by the static mode of Differential Global Positioning System (DGPS) to find the correct relative location with respect to earth coordinates. The MCDM process was used in conjunction with overlay weighted analysis based on the Analytical Hierarchy Process (AHP) technique to determine possible zones for acceptable constructions. To store more water in the agricultural watershed, a total of 19 new recharge structures—including check dams, stop dams, and storage dams—were suggested. Based on the physical observations, recommendations were also given regarding the state of repair needed for 41 structures that were already in the research area. Of the 41 structures, 8 required restoration and repair. The study’s findings showed that since UAVs and drones meet specific requirements, like precise ground control points (GCPs), high-quality photography, and scientific planning, they might be employed as the main source of topographic data. This research also corroborates that with the advancement of technology, UAV-driven digital elevation models have largely supplanted conventional topographic map-based approaches and has become more useful in landform analysis.