Beaches and dune belts cover 20% of the world's coastline and represent one of the most vulnerable ecosystem due to their unique environmental, microclimatic, and spatial conditions. The Coastal Dunes System (CDS) is characterized by definite ecosystem and geomorphological features, often threatened by the anthropogenic pressure and specific challenges related to habitat fragmentation and environment vulnerability. The present work focuses on the integration of Unmanned Aerial Vehicle (UAV) RGB and LiDAR data for the environmental analysis of a CDS, located within a high-density vegetation area in the municipality of Lesina (Foggia, Italy). The primary objective is to assess the vegetation distribution, monitoring metrics of psammofile species referred to one Natura 2000 sites in southern Italy, specifically IT9110015 – “Duna e lago di Lesina - Foce del Fortore”. In the study area, a major challenge for estimating vegetation volumes is the topographic analysis, as the dense vegetation matrix is too dense to let sensors signal go through. Hence, starting from the Digital Elevation Models (DEMs) and orthophoto obtained from the elaboration of the RGB/LiDAR data, it has been possible to distinguish the contribution of soil and vegetation by using the ExG spectral index. Consequently, by using the Natural Neighbor interpolation technique, it has been possible to reconstruct the Digital Terrain Model (DTM). Hence, the estimation of the total canopy volume was obtained from the Digital Difference Model (DDM), resulting approximately 42098.97 m3. The following validation process occur comparing UAV-derived DDM with a reference object, analyzed by Terrestrial Laser Scanner (TLS). In summary, this study concerns the following activities: (i) acquisition and elaboration of TLS LiDAR and UAV RGB/LiDAR data; (ii) spectral indices calculation; (iii) spatial analysis and interpolation techniques; (iv) Digital Difference Model (DDM) retrieval; (v) volumes calculation; (vi) DDM-derived volume validation by comparing TLS data.