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Habitat types represented include:
- seagrass beds
- sheltered intertidal mudflats
- sandy beaches
- subtidal soft sediments
- rocky intertidal shores.
The park forms part of the Western Port Ramsar site, and contains significant roosting and feeding sites for migratory waders. The intertidal mud flats extending from Rhyll to Newhaven are of state significance, and the area from Rhyll Inlet to Churchill Island is of national significance as part of a group of primary foraging sites for the 32 migratory waders found in Western Port (especially whimbrels and bartailed godwits).
Seagrasses include Swan Grass (Zostera muelleri), Heterozostera tasmanica (Eel Grass) and Seanymph seagrass (Amphibolis antarctica). Eel Grass is the dominant species in the deeper channels but is replaced by Swan Grass in the intertidal areas.
Seagrasses are food for Black Swans (Cygnus atratus) that eat large amounts of the thick root like rhizomes that run under the mud. As the seagrass passes through the body of the swan some nutrients are absorbed but most passes out of the swan to provide food for a wide range of invertebrates. Seanymph seagrasses with their wiry stems and grappling hook like seedlings are better suited to survival in area with greater wave intensity on rocky substrates.The seagrass habitats an important feeding area and nursery ground for a number of fish species. Some species that live in seagrass habitats at different stages of their lives include leather jackets, flounder, King George Whiting, Black Bream, garfish and flathead.