Mushroom Reef is the most striking piece of reef geology on the Mornington Peninsula: a flat, mushroom-shaped platform of ancient basalt exposed at low tide at Flinders Ocean Beach, with a 'stalk' of cobbles running out from the sand and interconnected bays and pools across its cap. Parks Victoria protects it and the surrounding waters – about 65 per cent of the sanctuary is subtidal – as the Mushroom Reef Marine Sanctuary, and it is a no-take area where fishing, collecting and feeding animals are all prohibited and divers must fly a flag and clean their gear. For snorkellers the platform at low tide is one of Victoria's best rock-pool sites, full of anemones, crabs, elephant snails, black-and-white seastars, saddled wrasse and cowfish.

For divers the interest is the subtidal basalt reef around and beyond the mushroom in 3–12 m: dark volcanic rock cut into crevices and gutters, roofed with brown algae, kelp and seagrass in the shallows and lined beneath with sponges, gorgonian fans, colonial ascidians and cup corals in the deeper gullies. Leatherjackets, morwongs, wrasse and cowfish are abundant because nothing is taken here; weedy seadragons live in the seagrass and kelp margins; crayfish and abalone are visible in numbers unusual for a shore dive; and dolphins, fur seals and, in winter, passing whales are seen from the reef. The basalt gives it a different feel from the limestone back beaches – harder edges, more relief, less sand – and the sanctuary status makes it the best place on the peninsula to see what an unfished reef looks like.

Its exposure is real: it is an unpatrolled ocean beach with strong currents around West Head and surge on the reef, and it is only for scuba on calm days with northerly winds. Flinders Pier is a kilometre away for the second dive. Mushroom Reef suits Open Water divers with some ocean experience on good days, snorkellers at low tide, and anyone interested in marine ecology.

From Flinders village take Golf Links Road (off Cook Street / Wood Street toward West Head) past the golf course to the car parks along Golf Links Road above the sanctuary, or the Flinders Ocean Beach car park about 300 m to the west; there is wheelchair access to the car park and viewing platform. A short sandy track and stairs lead down to the beach, a carry of 100–200 m. Enter from the sand beside the reef at mid to high tide (at low tide the mushroom is exposed and the subtidal reef is a long wade) and swim out over the reef edge.

Exit onto the beach; the toilet at Flinders Ocean Beach is permanently closed.

Mushroom Reef faces south-west into Bass Strait and needs offshore north-easterly to north-westerly winds and minimal swell; south-easterly to south-westerly winds and any rough weather make it undiveable, with surge over the reef even on calm-looking days. Strong currents run around West Head and across the reef on the tide, so dive around slack water and stay inside the reef. For snorkelling the sanctuary recommends two hours either side of low tide over the intertidal platform; for scuba, mid to high tide gives access to the subtidal reef.

It is an unpatrolled ocean beach.

Enter beside the reef near high tide, swim out along the edge of the mushroom to the subtidal basalt reef in 4–6 m, and work around the head of the reef through the crevices and kelp to a maximum of 10–12 m on the seaward side, keeping the reef on one shoulder. Turn at half gas or when current is felt, return inside the reef and exit onto the beach.

Bayplay and The Scuba Doctor run occasional guided snorkels and dives on calm days; Parks Victoria and Marine Care groups run snorkel events; otherwise independent divers and snorkellers.