The marine area of Mljet National Park is rich in a variety of life forms. Bivalves grow in large numbers in the Lakes due to suitable conditions. The most important are scallops (Pecten jacobaeus) and legally protected noble pen shell (Pinna nobilis), which is our biggest bivalve.   The scallop has two different shells connected by an elastic ring like a joint. The upper shell is convex and the bottom one is flat, both are folded with symmetrical radial ribs. Its colour is light brown or reddish depending on the environment it lives it. It is 8 to 15 cm long. It moves across the sea bottom by rapidly squeezing the water out of the shell opening. Malo jezero contains the largest population of scallops in the Adriatic with some of the oldest known specimens.

The noble pen shell lives at a depth of 2 to 30 meters on sandy and sand-muddy bottoms. The shape of its shell is like an isosceles triangle where the shortest side is shaped like an arch. The pointy part of the shell is buried in the sand and fixed with byssus fibers. Its shell is often covered with a multitude of sponges, algae, polychaete and tunicates. The shells of the largest specimens can reach as much as 1 meter. Irregular shaped pearls which have no commercial value can sometimes be found inside the shell. The density of the noble pen shell in Malo jezero is much higher compared to the rest of the Mediterranean. This is a strictly protected species.

The Lakes are also a home to an Aurelia genus jellyfish which has not been recorded anywhere else in the world so far. It can sometimes be noticed at the surface but it mostly stays in the deeper layers of the sea, feeding on plankton. Although it is quite large and can reach a size of up to 55 cm in diameter, it is completely harmless to people. Because of its large population, the jellyfish has a major impact on the trophic structure of the food chain in Veliko jezero.

Due to the specific environmental conditions in this area, Veliko jezero holds the largest recorded bushy coral reef (Cladocora caespitosa) in the world. The bushy coral or the Mediterranean pillow coral is a reef-building stone coral from the Faviidae family and it is endemic to the Mediterranean Sea. It lives in symbiosis with zooxanthellae which is why the colonies can be very large and sometimes develop large reef formations. The reef in Veliko jezero stretches over an area of 650m2 at a depth between 4 and 18 meters.