A luxury lodge with a mission in deepest Peru

The Amazon jungle may be the land of superlatives – the largest area of remaining pristine forest on the planet, threaded by one of the mightiest rivers in the world – but there's something dysfunctional about it. On the one hand, it's under greater pressure than ever; on the other, it has never been so well protected.

It's easy to gather some broad-picture impressions while peering from the window of an aeroplane: although the jungle is still breathtakingly vast, it wasn't possible to fly for more than five or six minutes – around 80km – without spotting some kind of man-made disturbance, usually a huge, denuded rectangular scar, the imprint of slash-and-burn ranchers clearing primary forest for cattle grazing or soya plantations. Today's Amazon stands at a junction, facing two very different futures. And at the riverbank of the sleepy, ramshackle jungle town of Puerto Maldonado, in the far south-east of Peru, that choice of direction takes on a physical reality.

The huge Madre de Dios river flows past the town from its source 5,780m high in the Andes, and onwards for 655km before joining a tributary of the Amazon. From the riverbank the boatmen can ferry you to one of two utterly contrasting worlds. Turn right, downstream, and you reach the tourist lodges that will serve up wildlife encounters you will never forget. Turn left, upstream, and you pass underneath the big red bridge that is part of the Inter-Oceanic highway linking Brazil's Atlantic coast with the Pacific ports of Peru. Many environmentalists fear that this 2,200km road will simply prove to be a convenient access route for logging companies. Slightly further upstream is the epicentre of the latest threat to the Amazon, the gold-mining industry.

So how does tourism square this circle of breathtaking beauty, magical encounters, grinding poverty and environmental apocalypse? Peru has no shortage of greenwash imposters – operators who promote their trips to the jungle as environmentally sustainable when they are anything but. But there are some shining lights, one of which is the Inkaterra Group, which has promoted environmentally sensitive tourism and funded scientific research for the past 35 years, and has gained the endorsement of the UN, the World Bank and the National Geographic Society.

The outfit was founded by a Peruvian national, José Koechlin, who opened his first lodge on the Amazon, Inkaterra Amazonica, in 1975. This has been steadily transformed into a luxury affair, well received by high-end tourists. Inkaterra also funds a non-profit institution devoted to research in the rainforest, cloud forest, the Andes and the Pacific, and has supported the reintroduction of the Andean spectacled bear, along with local community projects. The motivation for Koechlin is clear. In an interview with The Independent in 2008 he proclaimed that "for 30 years we have been collecting information on what is out there in the Amazonian rainforest ... not only to preserve it, but also to provide jobs".

Now Inkaterra has opened a second lodge close by, offering what look to be similar levels of comfort but in a more informal, relaxed setting, and with slightly lower prices. Eight kilometres downstream from Puerto Maldonado, Hacienda Concepció* is in a buffer zone, a semi-protected area between the wholly protected Tambopata National Park and the publicly accessible right shore of the Madre de Dios.

The lodge is set in the grounds of a 1950s Catholic mission, pioneered by a Spanish doctor seeking to improve the health of the indigenous people and finding a cure for leishmaniasis – a ghastly, ulcerous disease transmitted by sandflies that still periodically rises as an epidemic around the globe. (Celebrity traveller Ben Fogle said he was lucky to make a full recovery after catching the disease in Peru in 2009.) Much later, the mission was converted to a research station with the aid of the National Geographic Society, but today it has been rebuilt as a jungle retreat.

Mission control is a two-storey cedar lodge with palm-frond thatch, fitted with netting on all sides, a bar and lounge on the ground floor and eight rooms spread over both floors. A path leads from the lodge to a further seven stand-alone cabañas, with double beds, stylish wash basins, lake views and all the soft cotton linen you could wish for. All staff are Peruvian and most are local or from other jungle areas.

Most materials are sourced locally: cushions, mosquito nets and pillows are sewn in Puerto Maldonado, from where meat is also sourced. The rustic furniture is carved from second-hand ironwood, sourced from concessions where any felled tree must be replaced, says Gustavo, the lodge manager. Vegetables are harvested daily from Inkaterra's own farm downstream, while the food is washed in purified water.

Over three days here I had some of the most marvellous wildlife experiences of my life. You can pretty much guarantee seeing most animals on your wish-list within half a day – caimans, macaws, river otters, monkeys, bats, ultra-poisonous snakes.

The main course in this nature feast is Lake Sandoval, a dreamy, magical lake within the Tambopata Reserve, one of the most pristine, biodiverse areas on the planet. To reach its heart you must register at the ranger station, follow a well-laid path for two miles, then take a small fibreglass boat through narrow creeks. It's like being in a page of a geography textbook, for Sandoval is the classic oxbow lake, formed by the ever-changing course of the Madre de Dios.

Everywhere there were breathtakingly beautiful birds. Their song was miraculous. One, identified by my guide, Geraldine, as the screaming piha, sounded like a wolf-whistling Clanger. The oropendola's resembled the sonar of a submarine, and, true to its name, swung drunkenly on a branch as it sung. Then there was the ubiquitous morpho menelaus butterfly, an iridescent, flapping napkin larger than two cupped adult hands.

Leaving Sandoval, our pick-up boat to the lodge was delayed, so Geraldine suggested we walk the three kilometres back. Following little-trodden trails, we found ourselves surprising a dusky monkey with a baby, and saw hummingbirds, woodpeckers and a saddleback tamarin monkey, a brown-black ball of fur.

Later, we clambered up an old watch tower to the roof of the tree canopy. Here, as part of a UN-funded project, Inkaterra has constructed a tree-top walk, on rope bridges. It allows scientists to study and tourists to marvel at the flora and fauna that inhabit the clouds. If you have a head for heights, you can even overnight in a treehouse, but it's not for everyone as the bridges wobble and dip.

Treks tend to be sweaty, dehydrating affairs, though most last only a couple of hours and any mild discomfort was more than assuaged upon my return to the lodge. The lunchtime routine was typical. I'd shake off my wellies – provided by Inkaterra and, after mosquito repellent, the most indispensable piece of kit – and be greeted with a cool drink of crushed lemon.

In Lima, I had bought some tinned food, presuming rations would be meagre out here. Safe to say, the Spam stayed unopened. Inkaterra's food is mouthwatering: the self-taught chefs produce brilliant Italian, French and national dishes (though, thankfully, not guinea pig) such as bread made with yucca and spicy rice and fish. It all seemed like paradise.

Inkaterra is working hard, along with other conservation groups, to safeguard the Amazon, believing the country can enrich itself without widespread destruction. But upriver you find a very different view.

Gold has lured humans here since the conquistadors, and these two worlds exist cheek by jowl in Peru. For the tourist, there's no escaping them, and you'll see small-scale two-man mining operations all along the river banks. If men in Puerto Maldonado and further afield don't get work at a jungle lodge, they will turn to gold mining. In this kind of mining, sand and silt are sucked through what looks like a demented samovar; everything is then poured into an oil drum, along with mercury, to separate the ore. For greater effect, this cocktail is stirred by forearms or legs, raising disturbing health implications for the men even if these isolated operations seem to have relatively low-key environmental impacts.

Further upriver, and out of sight of tourists, it's another story. Recent US research by Duke University's Nicholas School of the Environment has linked the record global price for gold with a six-fold rise in deforestation in the floodplains of the Peruvian Amazon. It even outpaces settlement deforestation, as miners blast river banks and clear floodplain forests to expose potential gold-yielding gravel. The trouble with gold is that it can be mined with relatively low technology, making it accessible to unskilled workers. The result in places is an annihilated forest and ponds laden with mercury that can move up the food chain.

There's still hope, and a visit to the Amazon is still a breathtaking experience. Geraldine spoke in awed tones of non-contact tribes deep in the forest who have confounded anthropologists, and have somehow yet to encounter modern civilisation. But how do we know about them? They are sometimes spotted collecting turtle eggs by aircraft and helicopters conducting logging and drug patrols. The magic is being squeezed from all sides.

On my last evening I sat on a fallen tree trunk, switched off my torch, and listened to the cacophony around me. The pe-woop pe-woop of the blue-crowned motmot echoed through the trees, while the branches shook as unseen monkeys began their nocturnal jaunts and high jinks. There was the drumbeat of cicadas and an unidentified animal responsible for a noise that sounded like a whistling kettle left on the stove.

Can you put an economic price on all this? It has been done. One hectare of rainforest was once calculated by Dr Alwyn Gentry, a botanist, to offer an income of up to £6,000 a year from its fruits, medicines, tourism and sustainable timber. But cut it down for cattle grazing and the return is a one-off £20. Yet it's the latter economic case that seems, to the bafflement of environmentalists and sober economists, to prevail.

Travel essentials

Getting there

Mark Rowe travelled with Journey Latin America (020-8747 8315, journeylatinamerica.co.uk). A three-night stay at Hacienda Concepció* costs from £585, including return flights from Lima to Puerto Maldonado, return airport transfers, full board and excursions. International flights extra. There are no direct UK to Lima flights. From Heathrow, you can go with BA (0844 493 0787; ba.com) and partners American Airlines and Iberia – the former via Miami, the latter via Madrid. Air France (0870 142 4343; airfrance.co.uk) flies via Paris; KLM (08705 074074; klm.com) via Amsterdam.

Staying there

Hacienda Concepción (0808 101 2224; inkaterra.com). Doubles from US$308 full board.

Further information

Peru tourist board: peru.travel