Take a trip to Australia's secret marine wonderland

"A manta ray just surfaced, about 200ft to starboard." The calm voice of Carl, our dive master for the day, suggests this is by no means an unusual occurrence and certainly nothing to get worked up about. But I've never seen a manta ray before so I'm hopping around the boat as giddy as a schoolgirl.

"Where?" I yelp, jumping on to the starboard gunwale and scanning the water for any dark shape looming nearby. Then a pair of jet-black wingtips breaks the surface and a majestic creature is suddenly gliding towards us, its mouth agape as it trawls for plankton. These gentle giants are among an astonishing array of marine life that draws divers from all over the world to Ningaloo Reef.

Ningaloo begins at North West Cape by the town of Exmouth (population 2,500) in Western Australia and runs south for 160 miles before eventually petering out. In contrast to its more famous Queensland cousin, Ningaloo is a fringing reef, which means it lies much nearer to shore – as close as 100 yards in some places. Tropical reefs this accessible tend to suffer the impact of too much human activity, but Ningaloo's geographical isolation has allowed the marine environment to survive relatively intact.

Exmouth itself has no claims as a tourist attraction: three modest holiday resorts, two pubs and a handful of fishing, diving and whale-watching tour operators. But at this special place where the desert meets the reef, amenities are a secondary consideration. For divers (and their non-scuba dependent snorkelling companions), fishing enthusiasts, and those who come simply to revel in a feeling of complete remoteness from the rest of the world, Exmouth offers an experience perhaps not replicated anywhere.

The day of my manta ray encounter begins with a dive on Blizzard Ridge, a limestone plateau that is as flat as a counter-top, with small "bomboras" – protruding coral formations – lined up alongside like so many bar-stools. The spaces between the "bommies" shelter small groups of snapper, spangled emperor and coral trout, while closer inspection of the corals reveals more furtive creatures such as octopus and crayfish, as well as the two biggest moray eels I've ever seen.

The dive quickly turns into a procession of the oversized: the biggest white-tip reef shark I've seen, the biggest lionfish – even the biggest stingray, its 7ft span revealed as it lifts off from the sand and rockets away. I remind myself to keep a look-out for Ningaloo's smaller treasures, and it's not until we retrace our route back to the boat that I spy a couple of nudibranchs: molluscs that are tiny miracles of aesthetic design barely 2ins long, and which sport stripes of orange, black and royal blue.

Our next dive is at a site ominously named Labyrinth (in reality just a haphazard collection of bommies that all look much alike). A gentle current carries me over the top of three giant clams regally tinged with shades of purple and green, as well as several sea anemones and their inhabitant families of clownfish – endearing little fellows who guard their homes fiercely and are not above giving the fingers of nosey divers a nip. What at first I think is a moray eel winding its way among the bommies turns out to be a (highly venomous) olive sea-snake. Encounters with sea snakes are rare here, but from the moment it appears until we surface 15 minutes later the snake follows us everywhere, swimming behind a pair of flippers one moment, gliding between a pair of legs the next. Whenever we stop to examine a coral formation or peek under a ledge, the snake pauses too and fossicks about on the sea floor; then the moment we move off it looks up as if to say "Hey, where's everybody going?", and resumes its pursuit. The encounter bears out a shared perception among divers at Ningaloo that the marine animals here have not been threatened by humans, and so they react with curiosity rather than fear.

It's a strange feeling to be rounding off my scuba adventures with a dive not on the reef itself but off a long-abandoned pier. The US navy set up a base in Exmouth in 1967, but left in 1992. Their maintenance pier was left in the hands of security contractors who are still paid to keep it gated and guarded. Exmouth dive companies have controlled access to it, but private diving and fishing parties remain forbidden. It is now widely acknowledged as being among Australia's top five dive sites, which explains why I find myself clambering down a set of steel stairs in full scuba rig before taking a 10ft drop into the ocean.

Swimming through the superstructure of a pier is a lot like a wreck dive, only with girders and pylons instead of hatchways and railings. We descend past a school of barracuda hanging suspended in mid-water, looking menacing the way only barracuda can. Huge estuarine cod drift in and out of view, moray eels show their needle-like teeth from holes within the coral, crayfish wave feelers from beneath crevices and white-tip reef sharks glide over the sand. Even the pier's famed frogfish shows itself – its visage remarkably reminiscent of Australia's former prime minister John Howard, all rubbery lips and exuberant eyebrows. By the time we surface an hour later, I've counted more different species on a single dive than I'd hope to see in a dozen dives anywhere else.

As our dive group parted ways back in Exmouth, everyone was still gabbing about this or that creature they'd just seen for the first time. A German couple entreated the rest of us to return during the whale shark season from April to June, when a procession of the world's largest fish make their unhurried way along the coast, inhaling plankton by the ton.

Before leaving this far-flung corner of Western Australia, I'm up for two days of perfect isolation at Ningaloo Reef Retreat, a resort 30 miles out of town, well away from the modest bright lights of Exmouth. Paul, the owner, collects me in town and points out shallow bays for easy snorkelling as we drive along, before pulling up at the start of a sandy track that leads to the Reef Retreat. It's all of 100ft from the cluster of tent cabins to the beach and about a hundred more out to the coral. My cabin light and the hot water for my outback camping-style shower are both generated by a single solar cell, a fact that gives me a feeling of earth-loving satisfaction. I've never even heard of a gas-powered refrigerator, but there's one here. Fresh water is non-existent at this spot where the desert meets the sea, but a daily delivery from town takes care of everyone's needs. Food is likewise trucked in daily, and according to the guests' menu preference – snapper fillets, kangaroo steaks and lamb chops for the barbecue and Thai chicken curry are among the selections during my stay, and there's no shortage of salad and fresh fruit.

There are only six other guests, so it feels like a retreat from the rest of the world. It's nice too after wrangling heavy scuba gear all week to just slip on a mask and fins and potter about among the corals. And in between meals there's little else to do but spend quality time in a hammock time with a good book.

On my final afternoon, just before sunset, I pick up one of the resort's kayaks and paddle out for one last look at Ningaloo. And I'm suddenly struck by the thought that while the rest of the world has to make do without so much as one great reef, Australia has miraculously been blessed with two of them.

GETTING THERE

Qantas (0845 7747 767; www.qantas.co.uk) flies daily from Heathrow to Perth, via Singapore, from £680 return. Emirates (0870 243 2222; www.emirates.com), Singapore Airlines (0844 800 2380; www.singaporeair.co.uk), Cathay Pacific (020-8834 8888; www.cathaypacific.com) and Malaysia Airlines (0870 607 9090; www.malaysiaairlines.com) offer connections to Perth via a range of UK airports.

Exmouth is 720 miles north of Perth; two days' driving (or 24 hours on a bus) will get you there, but it's better to make a leisurely road-trip of it and explore along the way.

SkyWest (00 61 1300 660 088; www.skywest.com.au) flies daily from Perth to Exmouth.

STAYING THERE

Potshot Hotel Resort, Exmouth (00 61 8 9949 1200; www.potshotresort.com) offers a range of accommodation from self-contained apartments to campervan sites. Motel rooms start at A$140 (£63), apartments at A$150 (£67) and dorm beds at A$25 (£11).

Ningaloo Caravan & Holiday Resort (00 61 8 9949 2377; www.exmouthresort.com). Cabins start at A$115 (£51), two-bed apartments at A$150 (£67), and dorm beds at A$25 (£11), room only.

Ningaloo Reef Retreat (00 61 8 9949 1776; www.ningalooreefretreat.com). Double tents start at A$720 (£322) full board.

DIVING THERE

Exmouth Diving Centre (00 61 8 9949 1201; www.exmouthdiving.com.au) offers diving and snorkelling trips on Ningaloo; a half-day boat trip with two dives and scuba gear costs A$150 (£67). The dive centre's whale shark trips generally run from April to June. The price of A$350 (£156) per person includes the boat-trip, lunch and equipment and covers the cost of the spotter plane deployed to maximise the chances of an encounter.

RED TAPE & MORE INFORMATION

British passport-holders require a visa to visit Australia. These can be obtained electronically from the website of the Australian High Commission (Strand, London WC2B 4LA; 020-7379 4334): www.australia.org.uk. The cost for a three-month visa is A$75 (£34).

Tourism Western Australia: 00 61 8 9949 1176; www.westernaustralia.com.