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Habitat types represented in the park include seagrass beds, mangroves, sheltered intertidal mudflats, sandy beaches and subtidal soft sediments in tidal channels. The park's well developed tidal channel system of varying depth, profiles and orientations, contributes to the high diversity of habitats.

The north shore of French Island is one of the major areas of saltmarsh and mangrove fringe in Victoria and is of State geomorphological significance. These plants are unusual in that they are able to cope with the highly salty conditions of this environment. Mangroves are also able to cope with living in thick, airless mud.

The marine national park has extensive areas of seagrass (Heterozostera tasmanica and Zostera muellleri). Seagrasses have disappeared from more than 80 per cent of Western Port during the 1970 and 1980s and little of this has recovered. Despite small increases in recent years, seagrass loss still remains as a major concern for Western Port. Seagrasses are extremely important habitats and play a major role as nursery areas for many fish species, including commercially important species such as whiting.

The mudflats support a wide diversity of deposit feeding animals such as worms and bivalve molluscs like pippies. These animals convert the debris that accumulates in the bay into animal tissue which is then available as food for animals like birds and fish.

Western Port as a whole is of great importance as a bird habitat, with over 295 species recorded. These include extensive populations of Black Swans (Cygnus atratus), Pied Oystercatchers (Haematopus ostralegus) and Royal Spoonbills (Platalea regia). For many wader birds, the main habitat requirements are mudflats for foraging and high tide roosts where birds wait for the next feeding period.

Many of the migratory wader birds that spend summer in Victoria depend upon Western Port, and particularly the region now protected in the French Island Marine National Park. The area is used by up to 32 migratory bird species and is part of the Western Port Ramsar site. These birds migrate from the northern hemisphere and spend our summer feeding on the wide diversity of invertebrates found in the mudflats and seagrasses. Some of the notable migratory species include:

  • The Eastern Curlew (Numenius madagascariensis) -  non-breeding birds migrate from north-eastern Asia.
  • The Bar-tailed Godwit (Limosa lapponica) - breeds in Arctic regions of Eurasia and Alaska.
  • The Curlew Sandpiper (Calidris ferruginea) - breeds in the Arctic regions of eastern Siberia.

The marine national park includes the waters around Barralier Island, which is one of the bay's 13 high tide roosts and is particularly sensitive to disturbance.