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The habitat types represented within the park include:
- sandy beaches,
- intertidal and subtidal rocky reefs
- subtidal soft sediments.
The intertidal rock platforms are extensive and exhibit a diverse range of marine life. The subtidal rocky reefs include numerous microhabitats, extending several kilometres offshore in relatively shallow water.
The diversity of intertidal and shallow subtidal invertebrate fauna is the highest recorded in Victoria on sandstone. A high proportion of the common invertebrates occurring along the Victorian coast are found here. For example:
- seven of the eight species of brittle stars
- nine of 11 sea cucumbers
- eight of 11 barnacles
- all five sea anemones
- 15 of 20 chitons.
The underwater reefs here look different to those in other parts of Victoria. For example, crayweed, the large brown seaweed that covers many Victorian reefs, is mostly absent here. Instead, a multitude of more unusual plants and animals flourish. The species richness of the Bunurong seaweeds is comparatively high and includes green, blue-green, brown and encrusting coralline red algal species.
The subtidal marine flora of the area is characterised by a mixed group of brown algae consisting predominantly of:
- Acrocarpia paniculata
- Seiroccus axillaris
- Cystophora retorta
- Cystophora platylobium
- Cystophora moniliformis.
The seagrass Amphibolis antarctica is also an important component.
Invertebrates found in the subtidal zone include:
- Blacklip Abalone
- several species of crabs
- feather stars and brittle stars
- numerous sea snails
- small crustaceans.
The zone is dominated by macroalgae, particularly brown algae species, with an understorey of other green and red algae.
Besides the reefs, there are many other habitats at Bunurong.
Extensive intertidal rock platforms are covered in fields of Neptune's Necklace (a brown seaweed that looks like strings of beads), pink coralline algae, barnacles and a diverse range of marine molluscs.
Beds of Sea-nymph seagrass grow in the bays, with tough wiry stems and roots that can withstand the waves. Many smaller seaweeds and encrusting animals live on the stems and leaves. The sandy bays also host a specialised community of minute animals that feed on debris from broken pieces of seaweeds and seagrasses, and become an important food source for larger animals such as fish.
Several animals and plants have only been recorded in Victoria at Bunurong, and many others are at their most easterly location here, preferring the cool waters of Victoria's west coast. The coastline is also well known amongst marine naturalists for its diversity of flat 8-plated grazing molluscs known as chitons.
At least 87 species of fish have been recorded within the waters of Bunurong Marine National Park. Common species of fish sighted by recreational divers within the park include:
- Blue-throated Wrasse
- Common Bullseye
- Old Wife
- Gunns Leatherjacket
- Tasmanian Blenny
A range of pelagic species also use the area periodically, including:
- many species of shark (eg. Gummy Shark, School Shark, Common Saw Shark, Angel Shark and Elephant Shark)
- King George Whiting
Brightly coloured seastars, feather stars, crabs, large marine snails, and many smaller animals are plentiful here. Around the rocks at Eagles Nest and Twin Reefs, numerous Port Jackson Sharks rest under the ledges, rock lobsters fill the crevices and Zebra Fish, sweep and wrasse dart about the seaweed.Eagles Nest provides habitat for breeding peregrine falcons and hooded plovers. The park also adjoins a foreshore area consisting of dunes (in the west) and high cliffs (to the east) which support important remnant coastal and dune vegetation.