Nepean Bay is the sheltered water on the inside of Point Nepean, between the tip of the peninsula and Observatory Point, and it is where Portsea charters go when the Heads are not an option. The Scuba Doctor listing describes 'scattered reef, lots of fish and scattered wreck debris' in 1–12 m, 'lovely shallow clear water sheltered from all winds except northerlies', and notes that it is 'suitable for end-of-day diving' – the easy second dive after a wall, or the training dive when the swell is up outside.

The reef is a series of low limestone patches and kelp beds on a sand floor, some of them covered by sand for months at a time and then exposed again, with the deeper ground toward the entrance side of the bay. Because the whole of Point Nepean and its waters are within the marine national park, the fish life is recovering and the listing notes that 'fish populations are gradually recovering': old wives, sweep, wrasse, leatherjackets, magpie perch and scalyfin are abundant and approachable, cuttlefish are common in winter, and rays and Port Jackson sharks lie in the gutters. Seals from the point pass through.

The wreck debris is a reminder of where the bay is. The rocks of Point Nepean and Corsair Rock have claimed ships for two centuries, and the wreckage of several of them – most notably the clipper Empress of the Sea, deliberately beached and burned here in 1861 – lies in and around the bay; the Empress and the two shallow sub-sites on the inside of the point, Inner West and Inner East – Radar, are listed separately, as is Sweep Reef on the ocean side. Scuba Doctor also lists the Isabella Watson (1852) on 'Nepean Reef'. For a diver, Nepean Bay is a place to relax: shallow, clear, sheltered, full of fish and dived on the ebb so that the tide, if it is felt at all, sets back toward Portsea.

Boat access only – Point Nepean is a national park and the listing notes that shore diving is prohibited from the point. Charters from Portsea Pier (Dive Victoria Group, Bayplay) are 5–10 minutes west along the shore; Red Boats from Queenscliff about 15 minutes across the entrance. Private boats launch at Sorrento Boat Ramp (Point Nepean Road, all-tide, trailer parking) and run 15 minutes west past Portsea.

Nepean Bay is shallow and the boat anchors on sand outside the reef line or holds off; a dive flag is required and the pilot boats and ferry pass close to the bay.

Nepean Bay is 'sheltered from all winds except northerlies' (Scuba Doctor) and is the standard fallback when the Heads are unworkable, but the tide still runs through it: the Parks Victoria guide advises diving these reefs on the ebb, when the outgoing tide leaves the bay in relatively still water and any drift sets back toward Portsea rather than out through the entrance. Slack water at Port Phillip Heads does not coincide with high or low water: it falls roughly three hours after high or low water at Point Lonsdale, and the usable window is typically 20–40 minutes. Use the Ports Victoria / Port of Melbourne slack-water predictions for The Heads (also republished by charter operators and WillyWeather 'Rip Bank') rather than a standard tide table.

A northerly over about 15 knots puts a chop on the bay and cuts visibility; swell has little effect. Diveable year-round; clearest in autumn. Water 12–13 °C in winter, 17–19 °C in late summer.

Anchor on sand outside the reef on the ebb. Descend and work the scattered reef patches and kelp at 4–10 m in a loop, checking the sand between them for wreck debris and rays, and finish in the shallows under the boat; snorkellers cover the inner reef at 1–4 m. No navigation pressure – the bay is enclosed and the boat is always close.

Dive Victoria Group and Bayplay (Portsea) – frequent second dive, training and snorkel site, especially when the Heads are blown out; Red Boats (Queenscliff) – occasional; private boats from Sorrento.