Our vehicle comes to an abrupt stop. "There, now watch," says Josphat, my exacting young Masai guide. We cut the engine and the silence is acute. Josphat points out a cheetah's head in an ocean of golden grass. One minibus has already pulled up on another sandy track a few hundred metres away and four heads are craning out of the roof. We sit and watch for the cheetah. All of a sudden white minibuses crest the horizon in droves. We are in a stampede. Eight of them surround us. Within five minutes we have counted 30, the drivers communicating via radio to make sure their clients tick off "the big five". A cheetah will never kill like this; its prey will have been alerted. And if it has killed, the vehicles will make it blind to a subsequent hyena attack. But this cheetah is now nowhere to be seen. Undeterred, the minibus drivers start ploughing into the long grass. Eventually they give up. I ask if this happens often. Every day, Josphat says.

Josphat is a member of the Kenya Professional Safari Guides Association, which means he knows the Latin names and mating rituals of every animal in his domain. He is 27, small, intelligent and deeply serious about his work. He is accustomed to tracking animals and avoiding humans, but he is also proving adept at the inverse, showing me the "real" Masai Mara. One of the greatest natural spectacles on earth is under way. More than a million hungry wildebeest are on their way from Tanzania to Kenya's Mara National Reserve to raze tons of sweet red-oat grass. Primordial gnus are the stars of the show, but in supporting roles are a few hundred thousand zebras and half a million Thomson's gazelles; then there are the resident crocodiles, lions, hyenas, leopards and cheetahs.

A tourist plane lands in the Masai Mara. Photograph: Guillaume Bonn

Their show is in danger of being upstaged. Every year, thousands upon thousands of tourists descend on the Masai Mara to witness the migration. The resident human population is increasing; lodges are proliferating. Rampant corruption means money is not filtering down to the Masai population, who are increasingly turning to charcoal and arable farming to make ends meet. In short, mankind is in danger of squandering one of the most important habitats left in the world.

"It will not be long before it is gone, unless some drastic and urgent steps are taken now," says Joseph Ogutu, a scientist who has studied changes in the area's fauna for 24 years. The Masai Mara represents the northern quarter of the Serengeti ecosystem that stretches down into Tanzania. The wild animals that remain here require vast and various dispersal areas to survive drought, predators and human pressure. These safe havens are disappearing. Lodges surrounding the park have erected kilometres of electric fencing; lions have been known to use them to trap their prey. Shanty towns are developing fast, and some may soon be on the national grid. There are too many cows for not enough land, and wheat fields are advancing (wheat has become a swearword among conservationists). Human waste is being buried or dumped. The environment is displaying symptoms of its mismanagement. Algae are emerging in rivers upstream, a consequence of fertiliser use. The Mara river, where wildebeest cross from Tanzania, dried up completely in 2009, says Dickson Kaelo, a respected Masai guide. He recalls seeing scores of minibuses queueing to watch wildebeest splash through the water. But there was "just dust". Inside the treasured reserve, monkeys play with crisps packets. Even the predators' behaviour is changing. Malaika is a cheetah who will sit on the roof of your car; Josphat is disgusted by the guides who encourage her, to secure a good tip.

Kenya's economy is heavily reliant on tourism and the core area, the Mara National Reserve, generates an estimated £13m each year. The place projects a timelessness that speaks to notions of man's origins and the beginnings of time. But it also epitomises a modern conflict over land and resources playing out across Africa today.

Landowner Kaitet Ole Naingisa sips hot chocolate in a central Nairobi cafe. He has travelled to the capital to present his case to the commissioner of lands. He pulls his title deed from a brown A4 envelope. Naingisa's family had a plot close to the National Reserve in Siana where they had lived for more than 20 years, and where his 10 children are being schooled. Siana was one of many "group ranches", areas of communal land around the reserve, which have been subdivided among members in recent decades. It was this subdivision, locals say, that opened the door for the land-grabbing that is now epic in scale. When the land registry finally issued Naingisa with his title deeds last year, he got "this", he says, brandishing the embossed title deed to plot 366, far from his home, on unproductive land. The deed states his name as the land's original owner, but another name is semi-legible beneath it. There is a hole in the paper where someone has tried to rub it out. This is not his original land; the authorities have fiddled it, he says.

In battling for their rights, the Masai are seen as greedy by many conservationists, but most are not, an exasperated Josphat says: they just want their rightful share. The Masai occupied most of western Kenya at the turn of the 20th century, but disease, massive evictions by British colonialists and civil war reduced them to only 0.5% of the population. Centuries of survival in harsh lands gave them a strong sense of mutualism, but a culture of cronyism now pits the Masai against one another. The uneducated minority are represented, and exploited, by an educated few. There are countless lawsuits languishing in the courts and a number of unsolved, politically motivated murders. Paramilitary police have carried out forced evictions by night. People are bitter, and trust has eroded. Somali émigrés run thriving businesses in the Mara, because the Masai trust them more than Kenyan tribes.

A lion rests in a manmade quarry within the Masai Mara reserve. Photograph: Guillaume Bonn

Until last year, the Mara National Reserve, 371,000 acres of government-owned land, was administered by two different county councils. Now it is united under a new governor. "We call him the Big Fish," a young herdsman says.

One half of the administration had outsourced its management to a conservation group, one that received praise for its environmental work but faced allegations of corruption. Samuel Tunai, the "Big Fish", was on its board of directors. He holds a stake in more than 2,000 acres of prime land that were once part of the reserve but then given to the community to use. The land now boasts three luxury camps. There had also been allegations of corruption on the other side of the administration, and management was said to be worse. But now, under Kenya's new constitution, Tunai, as governor, is in charge of both administrations. He has rejected claims that his involvement in the Mara represents a conflict of interest. The Guardian's attempts to contact him proved unsuccessful.

A herd of tourist buses park in the Masai Mara to watch a river crossing. Photograph: Guillaume Bonn

Three decades ago, the Masai community gave president Daniel Arap Moi a parcel of land on the northern escarpment, a gesture that belonged to a more honourable era when "grabber" didn't feature in the local vernacular. Moi built a spectacular lodge with the only tarmac landing strip in the Mara. Today his presidential pied-à-terre, Ol Kurruk, has fallen into ruin. The buildings have either collapsed or been gutted by fire. Huge herds of giraffe and zebra have moved in. As we pick through the demolished rooms, small antelope, lizards and monkeys skitter away. Communities living on the escarpment fear Tunai plans to turn it into yet another luxury lodge.

"Today it's lodges, lodges, lodges. Everybody wants a lodge," Josphat says in despair. Some of those inside the reserve secure leases by greasing palms; others pay wardens for illegal permits, or start up as temporary camps and never leave. Outside the reserve it's easier. The first Chinese lodge is under construction on the south-eastern edge of the reserve. Its flat-pack cabins travelled 5,000 miles from China to be constructed on cleared forest. The minister for tourism said recently that of 108 tourist operations in the Mara area, only 29% were legal. Jake Grieves-Cook, a former chairman of the Kenya Tourist Board who owns a number of camps, estimates there are 7,000 tourist beds in the Mara ecosystem. If this is true, then in the past 10 years, despite a four-year moratorium on development, the number has almost trebled.

Fifty years after the process of dividing community lands began, it became evident that these traditional pastoral lands would turn into housing estates and farms if something didn't hold them together. A number of "conservancies" sprang up. These are privately managed reserves, funded directly by tourism, that lease land from communities to be set aside for wildlife. They increase the size of the protected area by 50%. Supporters argue that they will be enough to save the Mara; others say they are a sticking plaster and can support it for only so long.

Josphat and I venture out to Richard Branson's much-discussed new camp, which lies on its own conservancy away from the politics of the National Reserve. We eye the "tents" agog. They could feature in Star Wars, with four-metre pegs supporting futuristic domes. But their aspect is all natural. As we stand next to the infinity pool, a hyena obligingly comes to drink at the stream below. When almost 300 landowners of the surrounding Motorogi community were offered 3,500 shillings (£27) per hectare per year, they were delighted; the land was so overgrazed it looked worthless. Fast-forward five years and "you wouldn't recognise it", says Tarn Breedveld, Branson's handsome young manager. The story is the same across the conservancies: overgrazed land has recovered with only a few years of good management, and animals have come back in great numbers. For tourists, the conservancies give a flavour of what the Masai Mara was.

We drive between two conservancies with Grieves-Cook, an early pioneer of the community-owned model. Night falls and we become hopelessly lost. We drive through herds of buffalo and stop for hippopotamuses to cross the road. When we eventually arrive in camp we are greeted with a hero's welcome. The tented camps Grieves-Cook operates don't have menus or cash-bars. Seven hundred acres is budgeted per tent, and a game drive isn't a treasure hunt. Driving through Olare Orok conservancy, we sit in silence with a pride of lions for an hour as the sun goes down. Cubs tumble around like Andrex puppies and bloated females finish off a wildebeest as the lone male has a lie-down.

Go on safari, meaning "journey" in Swahili, with someone like Grieves-Cook and such mishaps and surprises will be the moments you remember best. In the early days, trailblazers took guests on a journey in every sense of the word. In the 1950s, the late Sydney Downey once burst every one of his tyres. His glamorous guests were made to stuff them with grass and bump along. Another time, Downey forgot all the food apart from a wheel of cheese. His guests gave him a silver plaque to commemorate "the great cheese safari". When Downey discovered someone was going to build a permanent structure in his beloved Mara he was "horrified", his daughter Margaret recalls. Keekorok Lodge opened in 1962 on Downey's favourite camping site. It is a 200-bed behemoth with tarmac roads and a swimming pool. At 4pm sharp, white minibuses charge out, taking guests on prosaic "game drives".

A dog roams through an illegal settlement in the Masai Mara. Photograph: Guillaume Bonn

Animal habitat is disappearing. On the banks of the Talek river, overlooking the National Reserve, you can get a room for only 300 shillings (£2.30) per night. Talek is an urban island in an expanse of protected land and the largest trading centre in the Mara. Filling stations open early, televisions blare out from restaurants and bars, and the sex workers open their doors at night. The abattoir does a roaring trade but its owner is nervous – he's waiting for the first lion to steal a carcass. There is no public waste management system in Talek and the roads in the town aren't really roads but rising layers of human detritus where there's a tacit agreement not to build.

North of Talek on the Narok road, an enterprising woman has set up an impromptu charcoal stall beneath the Mara North Conservancy sign. A 150-year-old acacia tree lies slain on its side, prey to the charcoal trade. Once you take out these trees, the land can go over to wheat. Wildlife pays around 3,000 shillings per hectare per year, but wheat farming pays 8,000-10,000. Masai society is increasingly monetised, steered by electronic communications, motorised transport and imported food. These people and many more are trying to make a living, and although the National Reserve makes millions, they're getting little from it. Without incentive to protect it, they are destroying it. A Japanese businessman has offered the council 42bn shillings (£235m) to relocate people on the edge of the reserve to 20km away, a consultant for the council says, which would mean more forced evictions and an uncomfortable new chapter in the battle for the Mara's billions.

Jackson Looseyia, a veteran guide of 26 years and presenter of the BBC's Big Cat Diaries, is between safaris. I have come to meet him in a private house owned by a wealthy Briton. Looseyia wears rubber sandals made from old tyres, a red-checked shuka, red dress and beaded belt. "I don't normally eat like this," he says, feigning embarrassment at the elegant meal laid on. I believe him. However much time he has spent around westerners, Looseyia is Masai to the core. What concerns him most about the future of the Mara is the rocketing value of land. Africa is rising, the media proclaim, but it is doing so unequally. Wealthy investors in the former Masai rangelands 30km south of Nairobi have driven land up to 12m shillings (£93,000) per acre. Both the Masai, who "suffered big time", Looseyia says, and the wildlife are gone. "It's a threat to conservation, it's a threat to the community. We are bordering the famous Masai Mara National Reserve. That in itself is gold. It could easily go," he says.

As well as the Serengeti wildebeest that convene every year in the National Reserve, around 300,000 wildebeest from Kenya's Loita plains used to arrive concurrently and mingle with their Tanzanian counterparts – the "northern migration". Calvin Cottar, whose family have been in the Mara for almost 100 years, has seen the Loita migration reduce by 90% to 30,000 animals in the past three decades. Wildlife populations crashed by up to 70% in that time, according to a Journal of Zoology study, while cows grazing illegally inside the reserve were up by 1,100%.

The Masai don't want to see their pastures become sweeping wheat fields. But wildlife on land comes with a risk to personal safety, loss of grazing, disease and death of livestock – and this should be compensated. Money from wildlife should go directly to the people affected, Looseyia says. Otherwise it will be lost, like America's 65 million wild bison: not one walks freely today. While the focus is on the spike in elephant and rhino poaching, Looseyia says lions and hyenas are disappearing at an alarming rate. "This is a home to these species. We have come to invade and as invaders we need to understand when to back off." People say lions sleep for many, many hours, Looseyia muses. "What I know is that when lions do not want to see you around, the easiest thing is to close their eyes. Yes, they sleep. But not as we think they sleep."

Looseyia likens expats in the Mara to the key that will turn on the engine, with their experience and funding. But the agent of change, the engine, can only be Kenyan. Looseyia's 20-year-old daughter is at university. "In an ideal Masai world she'd have three children by now." Women like her, he says, are the leaders of tomorrow.

That night, Josphat maintains a soft but lyrical commentary as we drive through the National Reserve for the last time, away from the setting sun. "That's a topi on a termite mound – see its dark legs?" he says. "That's a fish eagle." Then something catches my eye, a multitudinous and multicoloured herd. "What are those?" I ask. "Those," Josphat pauses, "are cows." Next to a ranger's post, 200 cows are inside the protected reserve at peak tourist time. If the council cannot enforce their rules, what hope is there for preserving half a million acres of ecosystem for generations to come?

• Watch an audio slideshow of Guillaume Bonn's photographs, narrated by Jackson Looseyia, at theguardian.com/weekend