Some 7,000 years ago rising sea levels separated Rottnest Island from the Australian mainland. The island is formed of limestone rocks with a thin covering of sand. The limestone base affects the types of plants and animals that can survive there, and the six major habitats: coastal, salt lakes, brackish swamps, woodlands, heath and settled areas. Salt lakes occupy ten percent of the area.
The limestone coral reef surrounding Rossnest grew approximately 100,000 years ago when the sea level was thought to be at least three metres higher than the present day. The Rossnest Island Marine Reserve has a far greater range of habitats, marine plants and animals than that of the adjacent mainland coastline.

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