In the swamp, the alligator is just for starters

From Chesapeake Bay to the Everglades, America's south-east brims with wetlands, the mushy coast flopping in and out, one creek after another cosseted by marshes and barrier islands. Canoe inland and, sooner or later, you will wind up at one of the most mysterious habitats of all – the blackwater swamp.

From Chesapeake Bay to the Everglades, America's south-east brims with wetlands, the mushy coast flopping in and out, one creek after another cosseted by marshes and barrier islands. Canoe inland and, sooner or later, you will wind up at one of the most mysterious habitats of all – the blackwater swamp.

Swamps in the US are mostly flooded woodland. But like Britain's bogs these soggy hideaways are dark, dank and eerie. Indeed, they once harboured dirty deeds. Europeans drove local tribes out of the swamps; and when rice made feudal South Carolina wealthy in the 1800s, plantation owners steered clear of their humid investments and let their African slaves work at the mosquito-ridden crop.

For modern swampies, blackwaters mean biodiversity and tranquillity. In the US, less than half of the original 215 million acres of swamps are intact, and the National Wildlife Federation estimates that 300,000 acres are disappearing yearly. But what Thoreau described as "America's dazzling jewel" somehow still exists.

For a gentle introduction to the swamps visit South Carolina's Audubon Swamp Garden, near Charleston. Here you can meet the eco-system's keystone species, the American alligator, at a safe distance on a boardwalk. On my visit, a few five-footers lounged about and one of them pounced for prey right beside the path.

Georgia's Okefenokee is the place to find your own 'gator. Paleo-Indians arrived here before 8,000BC, and it was the Seminoles settling in the swamp from the mid-1800s who called it Ouaquaphen-ogaw, or Land of Trembling Earth.

This landscape suits alligators, and with a population of nearly 13,000 in the 650sq-mile refuge, you're guaranteed a sighting. Starting from the Suwannee Canal entrance in our canoes, it was easy to spot the split-open rubbery eggshells. The young were out and about; tiny, yellow-and-black striped creatures that moaned like newborn puppies. The mothers responded by smacking into the water, then rising to the surface again to eye us up. The babies wriggled over their snouts.

Most of the time this crocodilian family member is superbly laid back. As you glide along, the glistening creatures shyly sink or bask, their lovely eyes staring at nothing in particular. I rammed my oar on to a black, snout-like hump to push the canoe back on course. Jaws dropped. "It's only a tree root," I shouted to Chip Campbell, my guide and the owner of Okefenokee Adventures. The lily tubers bear even more of a resemblance to half-submerged alligators.

Cypress trees moved into wetland niches such as these in the Cretaceous period, spreading eastwards – like the alligators' ancestors, the dinosaurs – from Wyoming. Where Wyoming was once swampland like the Carolinas, the south-east was submerged under the sea. But, unlike the northern states, the region escaped the last great ice sheet. Geologically stable, its species adapted to the nutrient-poor waters.

The wildlife here is truly strange: air-breathing fish such as bowfins, with lungs as well as gills, and Georgia's largest salamander, the aquatic two-toed amphiuma, which shuttles about on land when heavy showers fall. Exploring this sub-tropical waterworld amid crying herons, plopping turtles and creatures of a kind that otherwise existed only in your imagination leaves you wondering if Noah himself might hove into view.

We settled down to eat, with a seven-foot 'gator and his smaller friend beside our platform. The larger creature was clearly after titbits. "Fed by tourists, a real shame," said Chip. "It makes him dangerous, so he's likely to be destroyed." The alligator stayed all night: roughly, I guessed, three feet from my head. He was still there next morning and, luckily, so was I.

If anyone's at risk here, it is him and not us. Shot almost to extinction in the 1960s, but off the endangered list by 1987, alligators may yet fall to the state-revived "fun" harvests, carried out with a snatch hook and a large stick. This is nothing to do with "nuisance" alligators in the family pool: between 1980 and 2002, Georgia had only eight reported alligator attacks on people, and even those were said to have been the result of carelessness by humans.

Good, "green" guides all along the eastern seaboard are more than eager to get you sampling their swamps. At South Carolina's Ace Basin I visited a tidal freshwater swamp near the island homes of slave descendants, whose Gullah language is a Creole comprising mostly Bantu and Elizabethan English. Nearby was Bull Island with its red wolves, and Little Saint Simon's Island with armadillos and tiny yellow rat snakes which popped up and down between the duckboards.

Inland South Carolina has Congaree Swamp National Monument, an international biosphere reserve. When the water's up on this flood plain you can canoe through magical tree "cathedrals", meeting any of 178 bird species in the 22,000-acre park. The wildlife was in fine fettle. A Carolina wren gave off the biggest yell ever to come from such a scrap of a bird. Three turtles beat each other up below the boardwalk. "You're seeing primitive America," said the ranger, Fran Remetta.

Swamps sing at dawn and dusk. Cutting into Devil's Gut, in North Carolina's Roanoke refuge, we were serenaded by cicadas as the light faded. Beavers added a tail-slapping bass beat. At daybreak, the swamp sucked and slurped. Another noise – whining – was unmistakable. Yes, this is the home of 27 species of mosquito. "Different ones at different times of the day," said Don Gray, who organised the trip with Joe Jacob of Rock Rest Adventures.To the north, Merchants Mill Pond, Bennetts Creek and Lassiter Swamp are an extension, geologically, of the protected Great Dismal Swamp. You might see black bears and bobcats if you're lucky.

"Why save swamps?" I asked Joe. "They're worth £5,000 an acre a year in timber, hunt licences, sports, and the way they absorb floods," he said. "But most people value them just for this – de-stressing. As John Muir said of rivers, they flow not past but through us."

The Facts

Getting there

Pat Sinclair flew to the US with Continental Airlines (01293 776464; www.continental.com), which offers return flights from London Gatwick via Newark into Charleston and out of Raleigh from £511. Alamo (08705 994000; www.alamo.com) offers eight days car hire from £200.

Further information

South Carolina office of tourism (001 803 734 1700; www.DiscoverSouthCarolina.com). Georgia department of tourism (001 912 651 3160; www.georgia.org). North Carolina tourism (001 252 482 1585; www.visitnc.com).