Some coastal ecosystems are of remarkable ecological importance since they host a vast diversity of species, for all or part of their life cycle. However, they are currently under direct pressure from coastal human activities and climate change. In the Mediterranean Sea, these key-habitats notably include Posidonia meadows, but also the coralligenous habitat and hermella beds. These biogenic structures are the result of simultaneous construction and destruction activities by a wide range of organisms. Monitoring the dynamics of the volume and morphology of these reefs is therefore a powerful indicator of the ecological state of the constituting communities. ‘Structure-from-motion’ photogrammetry – unlike conventional on-site surveys – is a fast, non-invasive and unbiased imaging technique that allows the efficient topographical of these habitats. Like our two eyes, the shots taken by two synchronized cameras allow the reconstruction, after computer processing of the stereoscopic images, of a high-resolution 3D model of the habitats surveyed by the diver. The project focuses on the key-habitats on the coast of Lazio and the Tuscan archipelago in Italy. It will provide a better understanding of the interactions between the topology of the sites and the biological communities that develop there, and their fine evolution; essential data for the specific protection of these areas. Moreover, the visualizations resulting from the 3D models will be able to be used as a transversal tool for many research topics, as well as a vector of sensitization of the general public during “virtual dives” in video.