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From the plane we catch glimpses of the Urubamba River, below Machu Picchu, plunging thousands of feet, then snaking through an ocean of trees that spreads east until it is lost in haze—the Amazon, the world’s largest and most diverse rainforest. We land in the humid furnace of Puerto Maldonado, the fourth-largest city in the wooded eastern half of Peru, known as the selva (the jungle). The airport is full of foreign tourists, mostly European and American, in jungle safari garb, and the parking lot is packed with kitschy jungle safari buses with thatched roofs, waiting tochauffeur them to boats on the Tambopata River, 15 minutes from here. One or two planeloads of tourists a day are shuffled in and out of 15ecolodges with capacities of 16 to 60, or more.

My 11-year-old son, Zachary, and I are embarking on a more unusual adventure. We’re on our way to the Amazon Rainforest Conservation Center (ARCC), an ecolodge and research center located eight hours up the Rio de las Piedras, a left-bank tributary of the Madre de Dios that has almost no other ecotourism. Within a half-hour of landing, we are speeding down the Madre de Dios in a roofed-over, 50-foot boat with a 60-horsepower outboard engine. It’s a strong, brown river, but only one of the Amazon’s thousands of sub-tributaries.

The Amazon Rainforest Conservation Center was built, with financing from the U.S. conservation group Tropical Nature, by Pepe Moscoso Garcés, a strapping 41-year-old local Peruvian of European descent. Pepe is accompanying us with his 12-year-old son, Frank, a playmate for Zach. Also on board are Juan de Dios, the head of the guild of Puerto Maldonado ecotourist guides; an Ese’eja native woman named Daisy, who will be our cook; a Machiguena Indian named Narciso; nature photographer Mattias Klum; and his assistant, Lars-Magnus Edjeholm. There are 52 forest tribes in the selva speaking 25 different languages. The native people on the Rio de las Piedras are called the Yine or Piro. The rest of the boat is crammed with boxes full of fresh fruit and vegetables, meat, and drink that will enable us to live in style for the next five days.

We pass a small floating gold-mining operation that is sucking up the river bottom with a thick hose. Inside, in a room full of diesel smoke, shirtless men, glistening with sweat, are picking the mud over for nuggets or gold dust. Then we enter the mouth of the Rio de las Piedras, which is 100 yards wide after its 200-mile journey. The river is way down because the Amazon is experiencing the worst drought in its recorded history, and the rainy season is overdue. Tree trunks, snags, and the occasional sandbar that Narciso pries us off with his pole slow our progress. Narciso is a smallish, lean, muscular man who never speaks but is always there when you want him, and he wears a perpetual mischievous smirk.

For the first four hours few native trees are visible except on the inner banks of bends, where solid stands of cecropia and another pioneer species called pájaro bobo have sprouted in the mud precipitated from the slower water. The forest has been converted to plantations by homesteaders from the Andean highlands. In the early 1990s the government of Alberto Fujimori gave 74 acres, with 984 feet of river frontage and 3,280 feet back into the forest, to any family willing to make a go of it in the selva.

We pass through blizzards of lemon-lime and orange sulphur butterflies and small, striped brown swallow-tailed nymphalids known as many-banded daggerwings. Thousands upon thousands are puddling on exposed sandbars and on the lowered banks. “I have never seen so many butterflies,” says Pepe.

Two russet-backed oropendolas are flying around in panic as five black caracaras raid their sock nests. None of our field guides do justice to the extraordinary vocalizations of the oropendola; they sound like watery gurgles fired from a creaky slingshot.

The camp has screen walls, a thatched roof, and two rows of alcoves with beds canopied with mosquito netting. Pepe was clever to make use of one of these oxbows that the river abandoned for a new, faster route on its seaward descent. The lake is like a lost world, a teeming microcosm of one of the planet’s most intricate and complex ecosystems. Even in its present drought-stressed state, the biodiversity here is mind-boggling. Zach and I paddle a dugout in the failing light, looking for caimans and anacondas in the marsh grass that is closing in on the open water, but we see only a pair of sungrebes paddling around. Distant relatives of rails and coots, they are small and boldly patterned. After dark Zach shines his light on the blazing orange eyes of a yard-long caiman on the lake’s edge and catches an enormous canetoad.We put in at dusk at Tipishca Camp, a small overnight lodge Pepe built a few hundred yards in from the river on one of its cast-off loops that is now a small eyebrow-shaped lake. Something is missing: the searing pungency of leaves decomposing on the forest floor that is so characteristic of rainforests. In fact, there is no smell at all, only the crackle of shriveled leaves underfoot, and the usual birdsong that I’d expect after spending years traveling in the Amazon is much muted. Juan identifies the catcalls of a screaming piha; the low, minor-key melancholy whistles of a tinamou; the doglike yelps of a white-throated toucan; and the vocalizations of jacamars, trogons, wrens, antbirds, and nunbirds. But compared with the usual din, it’s eerily quiet. “The silence is because of the secas, the drought,” Pepe explains. “The last rain was two weeks ago, and before that there wasn’t a drop for two months straight. It is mid-September. The rainy season should have started by now.”

At 4:00 a.m. we are awakened by a chorus of red howler monkeys from the other side of the lake. It sounds like wind rushing through the portals of Hades. We continue upriver, passing an intently motionless white-necked heron standing knee-deep in water, then 20 jabiru storks having a confab on a sandbar. One of them seems to be their cacique and is strutting around like a dictator. Thirty red-and-green macaws, headed for their clay lick, overtake us. Every mile or two there is another flock of these glorious, large vermilion parrots, which Juan calls guacamayos rojos. This river should be called the Rio de los Guacamayos.

The last finca, or plantation, of the Andean homesteaders ends, and the river becomes pristine, a corridor winding between two walls of densely packed trees, some 130 feet tall. Juan points out a king vulture—huge, with a bare, highly colored blue and orange neck and face—a kestrellike plumbeous kite, a sunbittern, and a yellow-headed vulture. Rounding one bend, we find 30 swallow-tailed kites, more than I have ever seen in my whole life, circling gracefully over the water. White heads and underbellies sharply contrast with their black forked tails and outer wing feathers.

Pepe tells me he grew up on the edge of what is now Manu National Park, upriver from Maldonado. “My father was a logger.  I studied electric engineering in Cuzco, but there were no jobs, so I set myself up as a river merchant, running food and beer to gold miners up tributaries of the Madre de Dios. They paid me in gold, and by the time I was 24, I had a small fortune: $45,000.” But Pepe went through it all mounting expeditions during the next two years to look for the lost city of Paititi, the legendary Inca city in the jungle. All he found was a couple of stone towers. 

Ecotourism was beginning to boom in the selva, and for eight years he worked on the Tambopata for Rainforest Expeditions, “until I became�����ܰ��������—sickof it,” he continues. “Moving all those bodies in and out becomes like a human zoo. But I loved meeting people from all over the world and showing them the beauty and the richness of the forest. So I decided to start my own company with funding from Tropical Nature and a 40-year concession from the government for 15,000 acres on the Rio de las Piedras.” The land includes a large eyebrow lake, Lago Soledad (“solitude”), named for a little settlement of which there is no longer a trace. “We are taking a big risk, because the Las Piedras is in a free zone,” Pepe says. “There are no restrictions. The river turtles are not protected, and the loggers and Brazil-nut gatherers live off peccaries, tapirs, and macaws, whose flesh is unfortunately delicious.”

A small sign on a tree marks the ARCC’s boundary, and 10 minutes later we dock at an inconspicuous set of wooden stairs coming down to the water from a dark path that leads into an emerald-forest Eden. There are six bungalows set back from the lake and a large lodge with a kitchen, dining room, bar, and lounge. The facility has a capacity of 16, and after two years of business, it is hosting 200 guests a year. “I want to keep it a low-volume, high-quality experience—no more than 600 a year,” Pepe says.

The most visible and dramatic action is on the lake, which is ruled by three giant otters, seven feet long from snout to tail. They drape themselves like leopards on dead tree branches sticking up in the water, frolic incessantly, and cruise the lake with their heads held high, sending rings rippling out over the still surface. There are a few 12-foot caimans here, which look like floating logs, approaching imperceptibly until they’re within striking distance of their quarry.

The border of the lake is packed with soaring trees and shrubbery cabled with vines that sag with the vegetation of other plants using them for scaffolding. As we paddle along, a mixed troop of squirrel and brown capuchin monkeys comes out of the understory. One curious squirrel monkey teeters out to the tip of a branch, 10 feet from us. Seeming no less threatened by our approach, the hoatzins flap to a perch 50 feet away. They are primitive birds with unkempt cockades. Young hoatzins have claws on  their elbows to pull themselves up branches. We pass a wattled jacana picking its way over the vegetation tumbling into the water, and a rufescent tiger heron standing on a low branch a hundred feet from a juvenile agami heron. With its wispy, light-blue crest, glossy green and chestnut back, and long rapierlike bill, it is one of neotropical America’s most dazzling birds, as well as one of the rarest members of the heron tribe.

It rains hard through our second night, breaking the drought. By daybreak the forest has sprung back to life. Joyous bursts of birdsong blend with the pulsing quake of frogs and insects. Rising with the howlers, we head up the still mist-shrouded river to a ccollpa (clay lick) visited by half a dozen species of parrot. The ccollpa is a smectite- and bentonite-rich, yellow-brown cliff on a bluff 300 feet above a sweeping bend. Pepe has built a blind 150 feet from it, and we spend the morning inside being as quiet and still as possible. We watch a tapir swim across the river below, and, rounding the bend, a thatched peque peque, a river skiff with a lawn-mower engine, carrying a family of loggers with some beams in tow.

At about 6:30 a.m., 30 white-bellied parrots (actually golden-green), with a few mealy parrots mixed in, land on the cliff and peck out balls of clay. The clay is thought to help the parrots’ digestion, neutralizing the alkaloids and other toxins in the seeds they eat. At 7:00 two red-and-green macaws come flying up the bend and double back, apparently scouting out the situation. They fly over the blind several times, seeming to note that there are humans in it. The question is, what kind of humans: hunters or birdwatchers? They land in the crotch of a cecropia tree that is growing out of the cliff. We can see the red lines on their white cheeks.

More macaws arrive in twos and threes until there are 30 of them. Several couples hang upside down from branches and groom and snuggle, stealing glances at us. Then by turn they swoop down to the cliff and return to their perches with clay balls, which they hold in one foot and nibble. After half an hour they all leave, and it is the turn of a similar number of smaller scarlet macaws. At the ccollpa there seems to be a literal pecking order.

Zach and I walk along the six miles of trails that loop around the lake with Juan and Narciso, who moves slowly and quietly, pointing out things that Juan interprets for us. Juan could be mistaken for an Indian with his mixed Japanese and Brazilian parentage, but he is a modern, urban Peruvian. He is a step removed from the world of the forest, but he has fallen under its spell and is good at spotting big birds like a Spix’s guan (a dark-brown, turkeylike bird with a featherless ruby-red throat), the razor-billed curas-sow (sheeny steel-black with a red bill), and a herd of collared peccaries that we creep up on and watch from behind a huge garlic tree until they sense our presence and bolt. He shows us medicinal plants for treating arthritis and rheumatism, diarrhea and constipation, kidney and prostate ailments, hangover, headache, and fever, as well as the cashapona,or walking palm, with a mesh of thin, splaying prop roots that, like the adjustable legs of a tripod, move the slender, straight trunk around to give it the best shot at the sunlight.

Zachary is focused on the forest floor. He notices things that elude even Narciso, like a yellow-footed tortoise and a five-inch-long baby fer-de-lance, the snake responsible for the greatest number of fatal bites in the Americas. Juan and Narciso agree it is a type of fer-de-lance known as thejergonsacha. Its dark- and light-gray diamonds blend perfectly with the sun-mottled leaf litter. Narciso nudges it with a stick, and it plays dead.

Zach picks up a batrachian the size of a fingernail—a toad, he pronounces. How do you know? I ask. “Frogs are wet, and toads pee on you,” he says. He discerns a nightjar so well camouflaged among the leaves that it is only an outline. You could spend your life—and some do—studying just one category of the organisms on the forest floor: the seeds, the snails, the spiders, the beetles, the ants, the sapitos and the �����Ծ��ٲ���—the little toads and frogs. On a fallen tree we find a rubbery pink earlobe-shaped fungus that Narciso says is delicious. Iridescent blue morpho butterflies patrol the forest, flashing creamy blue. Resting on a leaf is a small blowtorch-blue metalmark butterfly with red along its hind wing.

A whole set of different life-forms inhabits the canopy. Pepe has built a platform 130 feet up in the crown of a massive ironwood tree that we reach by being hauled up one at a time in a canvas chair by everyone below. As I rise above the lake I can see an unbroken sea of green spreading 100 miles north to the Acre River, the border with Brazil. I have an urge to just take off into it with Zach, Narciso, and Juan. We could probably reach the river in four days.

When I first set foot in the Amazon 25 years ago to write about this incomparable, incomprehensible wilderness, a fire bigger than Belgium was raging out of control. The forest was being cleared, and its flora and fauna, much of which is still uncatalogued, was going up in smoke in order to produce a few years’ worth of beef. The land would then be abandoned, to bake into brick-hard laterite.

The assault has continued unabated, and 18 percent of the forest has disappeared in 50 years. A sophisticated satellite system monitors the clear-cutting and the fires, and laws restricting deforestation are in place, but stopping it is another matter.

Still, the Amazon rainforest is so enormous that 82 percent of it is estimated to be, more or less, intact. Now there is another threat, more remote but no less devastating, as became evident when we flew over the Andes. The mountains looked like melting ice cream cones, their snow and ice reduced to small patches. The Peruvian National Council for the Environment has predicted that there will be no glaciers in Peru by 2020. All the world’s snow and ice is melting, but none so fast as tropical glaciers and ice fields. What will become of the Amazon with no snowmelt to feed its headwaters, and ever decreasing rainfall? Will it be a savanna again as it was 100,000 years ago?

In fact, the dehydration of the Amazon rainforest is already under way. While we were able to reach the ARCC, 40,000 ccaboclos, the mestizo backwoods people of the Brazilian Amazon, were stranded up rivers that had gone dry. The waterways are still the only roads in most of the Amazon valley. The world’s land surface is progressively dessicating as a result of global warming—even here, one of the wettest places of all.

And in a few years theInteroceánica highway will be completed, providing long-sought (and long-fought by conservationists) access to the Pacific and Asian markets for the Amazon’s wood and minerals. Puerto Maldonado will be overrun with marginal Brazilians, Pepe predicts—the homeless from cities who are already pouring into the Madre de Dios region. “Maybe I will move out to the ARCC and live there full-time,” he says. Every day trucks and boats bring more people with visions of El Dorado, carrying all they own in a tote bag to this fast-growing city of 50,000. Most of them will start out trying their luck at gold mining and end up cutting trees down for one of the lumber companies or collecting Brazil nuts. So if you want to experience the Amazon, you’d better get there fast, and I can’t think of anywhere better than Pepe’s five-star gem.

This story originally ran in the July-August 2006 issue as "Last Resort."