Unmanned aerial vehicles (UAVs) and unmanned surface vehicles (USVs) are becoming an effective methods for both environmental assessment and monitoring. UAVs commonly known as “drones” are aircrafts controlled remotely. USVs instead, can be defined as unmanned vehicles which perform tasks without any human intervention. Further development of these tools are expected to produce great benefits, such as lower operation costs, improved personnel safety and security, extended operational range and precision, greater autonomy, as well as increased accessibility in sophisticated environments. For this purpose, during 2017 we have performed a morphometric and bathymetric maps in Alpine lakes of Piedmont (Balma Lake, Cottian Alps) and Friuli-Venezia Giulia (Dimon Lake, Carnic Alps) using drones and an equipped boat with a fishfinder. The operations may be summarized in three steps: 1) creation of a topographical network in order to obtain a unique coordinated system for each lake; 2) aero-photogrammetrical surveys of the terrestrial area; 3) bathymetric surveys. After data processing we have obtained digital orthophotographs, contours and DTM (Digital Terrain Model) for the terrestrial area and the depth and volume of each lake. Accordingly, drones represent a potential role in the future management and conservation of ecosystems.