The habitats of this marine protected area consist of alternating rocky areas, seagrass beds, debris deposits, escarpments and depressions.

Although characterised by the rocky shoal, the seabed of this marine area is heterogeneous – full of ravines, escarpments, deposits and depressions, and therefore rich in biodiversity. It is also characterised by the presence of extensive Posidonia oceanica meadows that cover almost the entire surface of the area down to a depth of 20–25 metres, where they are gradually replaced by extensive coral reefs dominated by white gorgonian (Eunicella singularis), which in turn slope down to sandy seabeds featuring the benthic communities of the deeper marine environments typical of coastal detritus.

The Secche della Meloria therefore feature a consistent richness of species; indeed, its waters are home to numerous plant and animal populations. Faunal groups that can be observed in the marine environment of the Secche include: sponges, crustaceans, polychaetes, bryozoans, molluscs, tunicates, jellyfish, actinias, corals, starfish, and all the main species of fish found in the demersal zone, such as: damselfish, goatfishes, various species of wrasse, salema, Diplodus, East Atlantic peacock wrasse, dentex, sand steenbras, scorpionfish and syngnathids, as well as the largest and most representative species such as moray eels and the rarest ones such as the dusky grouper.