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The diverse geology of the sanctuary provides a variety of habitats including sponge gardens on the deeper reef, intertidal reef, rockpools, boulder fields and sandy beaches.

The large brown kelps, Durvillea and Phyllospora are the dominant plants growing on the reef and on the large rocks. The kelps provide shelter for a range of invertebrates including sponges, hydrozoans, gorgonians, yellow zooanthids, stony coral, lace bryozoans, green and black lipped abalone, nudibranchs, rock lobsters, hermit crabs, mosaic sea star, feather stars and sea tulips.

The shore rock platforms are covered in swathes of Neptune's Necklace, a brown algae that looks like strings of beads. The deeper rock pools are full of life including octopus, decorator crabs, chitons and schools of tiny silver fish.

The offshore rocks are fringed by swirling Bull Kelp, which thrives in the breaking waves. Colourful sea-tulips and encrusting sponges grow on the rocks. Blue Throated Wrasse, Rosy Wrasse and Sea Sweep are common fish. Schools of Yellow-eyed Mullet swim by. There are Cat Sharks in the kelp and stingarees, skates and rays on the sand.

Port Jackson Sharks can be seen resting in a sandy corral past Eagle Rock. These prehistoric-looking sharks with a crested head have rows of small pointed teeth that are used to crush pipis and other molluscs that they forage from the sand, as well as urchins and seastars from the reef.