Due to the variety and richness of species, the most ecologically interesting areas from the underwater point of view are on small rock emergencies in the channel between Tavolara and Molara over 25 m. of depth. The coral habitat of Tavolara is clearly defined by gorgonians (Paramuricea clavata and Eunicella verrucosa), large sponges (Axinella polipoides, Spongia agaricina) and by “black corals” (Gerardia savaglia), a typical exacorals of deep sea; Corallium rubrum is absent, a widespread species even at low depth along the western coasts of Sardinia. The uniqueness of the Tavolara marine protected area is to offer, within the first 25 m. of depth, a variety of scenarios and populations so wide as to represent a synthesis of what the Mediterranean can offer. The growth of tourism and the moderate increase in sedimentation with the consequent slow regression of the Posidonia prairie are for now signs of a potential degradation, but not yet certainly a sign of a tendency to worsening. In this sense, the establishment of a protected marine area certainly guarantees a first step in managing the natural resources of this incredible reservoir of species now rare in other areas of the Mediterranean.

The seabed of the southern slope is characterized by the cliff environment, in some points it goes down straight to the depth of 22 m. At the foot of the wall, large landslides of boulders, grazed by sea urchins, alternate with areas colonized by Posidonia oceanica. Small karst ducts open at various points creating typical cave environments where the magnose (Scyllarides latus) reproduce.
The northern seabed is characterized by landslides. It is a relatively shallow area, which ends on a detrital plain covered with Posidonia meadows. In correspondence of the Punta del Papa, from 42 meters from the bottom three submarine spiers rise, the highest reaches 15 from the surface. This pinacle is constantly surrounded by clouds of castagnole, ready to open and immediately regroup for the frequent arrival of voracious amberjacks. Down from the ridge of the shoal, descending towards the northwest, the large paramuricee fans open up among swarms of red chestnut trees. The light of the torches brings out the bright red of the colonies; many have a yellow variant and the visual impact is even greater. Along two other lower pinnacles, also covered by gorgonians, we reach a large coralligenous area. Not infrequently, on the seabed, they can see groupers and shoals of snappers.

Remarkably different from that of Tavolara is the underwater landscape that is found around these two islands. Granites reproduce underwater scenarios under water. Large cracked rock panettone, pierced and rich in tafoni (erosion cavities) characterize the seabed between Molara and Tavolara. The dried Fico is a typical example of this kind of rocky environment. The granite covered with a thin felt of algae, hosts several colonies of hydrozoans (close relatives of corals and jellyfish), populated in turn by colorful nudibranchs (shell-less gastropod molluscs characterized by bright colors). Corvina and groupers are common in cracks and crevices. More deeply intricate coralligenous constructions give shelter to groupers, sea bream and lobster. From Molara to Molarotto, the rounded shapes are replaced by an underwater landscape bristling with spiers that alternate with large areas of detritus and posidonia where Pinna nobilis meets.