Beaches and soft substrates form a distinctive group of marine habitats with their own suites of organisms. The sands in west and central Victoria are derived from the shells and skeletons of living organisms, while the yellow quartzose sands in the east were eroded from Devonian granite. Intertidal mud and sand flats are best developed in Port Phillip Bay, Western Port and Corner Inlet, where they cover large areas at low tide.

The tides plays a major role in structuring and nurturing these habitats. Subtidal sandy substrates occur along much of the open coast, as well as in Port Phillip Bay, Anderson Inlet and Shallow Inlet, but muddy subtidal substrates are restricted to sheltered embayments and deeper waters offshore. The soft substrates in deeper, subtidal waters support some of the most diverse marine communities; a few square metres of sand can contain over 570 species of macro-invertebrates.

Microscopic diatoms are the only plants to thrive on a beach. Small sea-fleas, pill-bugs, pipis and beach worms predominate in the splash zone, while bacteria, protozoa and nematode worms exist in the spaces between the sand grains. Silver Gulls are the most common of the larger animals, but other birds such as Sooty Oystercatchers and Pacific Gulls are also common. Algae washed up onto the beach provide the diet for a number of other animals, including beetles, sandhoppers, kelp flies and small crustaceans.

Animals such as Soldier Crabs, gastropod snails, marine worms and pipis inhabit intertidal sand flats, while mud flats support molluscs such as tellins, lantern shells and the Mud Ark, and crustaceans such as the Semaphore Crab and Ghost Yabby. Many fish move in over intertidal flats during high tides, particularly the Smooth Toadfish, stingarees, King George Whiting and Greenback Flounder. Victorian mud flats are also home to a wader bird community of international significance. Amongst the most numerous are the Eastern Curlew, Curlew Sandpiper, Red-necked Stint and Bar-tailed Godwit. Anglers collect intertidal invertebrates for bait, particularly pipis, large polychaetes and yabbies.

Soft subtidal sediments commonly support seapens, ascidians, hydroids, bryozoans and large, diverse sponge gardens. The animals within the sediment are dominated by marine worms and crustaceans. Subordinate groups are bivalves, brittle stars, holothurians, sea-urchins, gastropods, nematodes and nemerteans. Scallops inhabit fine sandy bottoms in Port Phillip Bay and in eastern Bass Strait. Fish include flatheads, whiting, flounder and sharks. Many introduced species have become established in subtidal soft sediments, where they are among the most abundant species.

The major pressures on beaches and soft substrates come from harvesting, the alteration of natural sedimentation regimes by coastal developments, bait collection, inappropriately placed structures, bottom trawling and dredging, boat traffic, trampling, and the introduction of exotic organisms.