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There are rich intertidal and subtidal invertebrate communities, dramatic underwater arches, canyons, fissures, gutters and deep sloping reefs.

The wild and powerful Southern Ocean that sculpts the area's limestone landscape also shrouds a remarkable seascape beneath the waves; a submarine labyrinth of towering canyons, caves, arches and walls. These natural features are festooned with colourful seaweed and sponge 'gardens', resident schools of reef fish, such as sweep, gliding above and the occasional visit by an Australian Fur Seal.
The marine environment of the Twelve Apostles Marine National Park is characteristic of the surrounding area from Childers Cove (east of Warrnambool) to Gibson's Steps, which has the highest diversity of intertidal and subtidal invertebrates on limestone in Victoria, as well as supporting a diverse range of fish.

From the cliffs you can see the thick brown fronds of Bull Kelp (Durvillea potatorum) attached to the rocks near the low tide mark, swirling in the ocean swell. Southern Giant Kelp forms forests at some locations that reach the surface from 10 metres in depth. Lobster, abalone and sea urchins are common underneath the thick kelp canopy.

Offshore reefs (30-60 metres deep) are known to support sponge 'gardens' with colourful and varied sponges, sea squirts and bryozoans that shelter many invertebrate animals including sea-spiders, beautiful sea slugs (or nudibranchs) and a diverse range of seasnails and seastars.

Little Penguins feed in the park and nest in caves below the Twelve Apostles. Patient observation just after dark or in the early morning will allow visitors to view these birds from the platforms at the 12 Apostles.

Geological, hydrological and landform features

The Twelve Apostle Marine National Park contains various geological rock types, including limestone, calcarenite, mudstone and sandstone adding to the complexity of the substrate and the range of rocky habitats available. These include platforms with shallow fissures and gutters, small rounded boulders and heavy reefs with sharp steeply sloping ridges greater than two metres in height, some with narrow crevices, and others with wide sand filled gutters. Dramatic arches, walls, caves and canyons are also present.

The Twelve Apostles Marine National Park represents habitats of the cooler waters of western Victoria. However, the most obvious environmental factor is the energy of the waves. The sea is seldom calm with waves pounding in every 10 to 16 seconds from the Southern Ocean. Away from the coast, the seafloor is mainly low rocky reef, with extensive areas of sand and shell rubble.