Macquarie Island and the surrounding region have unique geological characteristics. The island's orientation and the submerged Macquarie Ridge together act as a major barrier to the Antarctic Circumpolar Current, Earth's largest and most important oceanic current.
The Macquarie Island region is important for seabirds and seals that breed on the island and forage in the reserve. The reserve includes two habitat protection zones that were established to protect the habitat of seabirds and seals, and the benthic and pelagic fauna that depend on the area. The northern habitat protection zone includes a foraging area for fur seals (New Zealand, antarctic and subantarctic fur seals). The southern habitat protection zone includes foraging area for penguins during the breeding season, and it is used by many penguin species to transit to and from more southerly waters.
A number of species found in the Macquarie Island region, including five albatross species, four penguin species and two seal species, are under local or global threat, and because most of these species require extremely large migratory or foraging ranges, protection of their critical feeding and migratory areas has international significance.
Although the timing of many species seasonal occupation of the region and their behaviour while onshore are well documented, the behaviour of these animals while in the marine environment or outside breeding seasons requires further research.
The Macquarie Island Commonwealth Marine Reserve includes a portion of the Macquarie Island World Heritage Area, which extends from the shore to 12 nm and, accordingly, the Commonwealth has jurisdiction over waters from 3-12 nm.