Lakes play an important role in providing various ecosystem services. However, stressors such as climate change, land use, or land-cover change threaten the ecological functions of lakes. National and international legislations address these threats and establish consistent, long-term monitoring schemes. Remote sensing techniques based on the use of Unmanned Aerial Vehicles (UAV) have recently been demonstrated to provide accurate and low-cost spatio-temporal views for the assessment of the ecological status of aquatic ecosystems and the identification of areas at risk of contamination. Few studies have been carried out so far on the employment of these tools in the monitoring of lakes. Therefore, high-resolution UAV surveys were used to analyse and evaluate natural and anthropogenic impacts on the habitat status of a volcanic lake in a protected area. Five UAV flights took place during a year-long cycle (November 2020 to November 2021) in a volcanic lake located in southern Italy. For each flight performance, an orthomosaic of georeferenced RGB images was obtained, and the different features of interest were monitored and quantified using automated processing in a GIS environment. The UAV images made it possible not only to estimate the flooded shores but also to detect the impact of human-made structures and infrastructures on the lagoon environment. It has been possible to observe how the rapid changes in lake-water level have led to the submersion of about 90.000 m2 of terrain in winter, causing the fragmentation and degradation of habitats, while the connectivity of the natural ecosystem has been threatened by the presence of the road around the lake. The proposed methodology is rather simple and easily replicable by decision makers and local administrators and can be useful for choosing the best restoration interventions.