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Point Cook is a low rainfall area and the soil has a relatively high salt content. The natural vegetation at the time of European arrival comprised scattered clumps of trees, grasses and shrubs, frequently burned by the Aboriginal inhabitants. Extensive areas of saltmarsh vegetation grew in wetter areas close to the coast. There was a band of bush, probably wattles and shrub species, inland from the beach. This was known as the Point Cook forest and was felled as the area was settled.

The present day vegetation of Point Cooke is largely remnant basalt plains grassland, with areas of coastal salt marsh, grassy wetland and sedgeland. There are several natural waterbodies in the park supporting aquatic species. A notable plant found on the shores of the highly saline RAAF Lake at Point Cooke is the Chaffy Saw-sedge, which provides habitat for the rare Altona Skipper Butterfly. Selected sites in the park are now being planted with trees grown from seed collected from remaining natural specimens.


Over 250 fauna species have been recorded at Point Cook Coastal Park. During summer, visiting migratory birds move between the wetlands and saltmarsh at Point Cook, the beach sand flats and Cheetham Wetlands, depending on the tides. The endangered Orange-bellied Parrot is known to feed in the saltmarsh at Point Cooke. The Double-banded Plover flies from New Zealand to spend the winter in Australia, and the Eastern Golden Plover migrates here from Siberia and Alaska.

The marine reserve helps preserve the diverse flora and fauna of the reef. It is one of the last relatively unspoiled reef ecosystems in the bay and is an important feeding ground for sea birds and a refuge for marine life.