Unmanned aerial vehicles (drones) have been increasingly used in environmental research in recent years. In a relatively short time, they have become an accessible and cost-effective tool with many emerging applications in the field of environmental monitoring and biodiversity conservation. Drones equipped with multispectral cameras, capturing images in different light spectra, and thermal cameras are of great use for field studies and can produce cartographic data with high accuracy for early analysis of the state of ecosystems and habitats, the dynamics and changes of biodiversity, mapping and development of 3D models of habitats. The Veleka River Estuary (Strandzha, Bulgaria) is a protected area with a high conservation status, which is subject to increasing anthropogenic impact - bathing, sunbathing, water sports, fishing, motor boats, canoeing, etc. This creates prerequisites for increased population of habitats and population of endangered and vulnerable risks from wild flora and fauna. The basis of the monitoring study of the anthropogenic load in the area was used drone Phantom 4 multispectral, filmed with a multispectral camera, shooting in 5 different light spectra. In addition, some indices can be followed, such as NDVI - used to determine the health status of plants, to depict phenological changes, to assess green biomass. GNDVI - is a vegetation index for assessing photosynthetic activity and is often used to determine the absorption of water and nitrogen in the plant cover. Other indices that can be calculated from photos with a multispectral camera are LCI, NDRE, OSAVI. Through them, the state of the plant cover and the habitat as a whole can be monitored, both currently and over a long period of time. The photographs were used to track the dynamics of the abiotic and biotic components of the landscape, as well as to map the Veleka River estuary with long-term monitoring.