Pianosa Island consists of a limestone plateau substrate. The vegetation, in some areas, has been degraded and replaced by agricultural cultivation and pastures by the penal colony present on the island. The presence of this colony makes the island almost inaccessible.
The seabedssurrounding the island degrade slowly, allowing the development of Posidonia oceanica meadows, while rocky substrate areas are limited, especially in the shallows on the eastern side of the island. There are two small submerged cavities on the Marchese and Scola shallows.
In the western part of the island, some forms of vegetation survive, such as woods of juniper, brushwoods, and garigues. This area host the most significant insular flora, including endemic, rare, and phytogeographically interesting species. The island is also important for the nesting of rare bird species, as the lack of disturbances and the low presence of crops and pastures make it a place of great interest for migratory bird stopovers and wintering.