Nearly 13,000ft up in the foothills of the Himalayas, Amod Panwar, an Indian hotel owner and devout Hindu, reverently places offerings of almonds, sultanas and a coconut into the water cascading from an icy cavern known as Gaumukh, the “cow’s mouth”.

As dusk falls over the snow-capped peaks, a block of ice the size of a house breaks from the glacier and plunges into the stream with a roar, sending me scurrying for safety across the grey stones of the riverbank. Panwar, my guide for the gruelling high-altitude trek from Gangotri in northern India, is undeterred. He continues his devotions, strips off his clothes and immerses himself in water flecked with shards of ice. Only when we have filled plastic bottles with the holy liquid to take home in our backpacks do we walk downhill to the isolated ashram where we will take sweet tea and shelter in the cold October night.

Gaumukh, the source of the River Ganges, is one of the most sacred places in Hinduism. But in truth the entire river, flowing for more than 2,500km across north India from the mountainous haunts of the snow leopard (we see prints on the way down) to the tiger-infested mangrove swamps of the Bay of Bengal, is holy. Ma Ganga or Mother Ganges, described by Harvard religious scholar Diana Eck as “the archetype of sacred waters”, is worshipped as a goddess by Hindus worldwide. Her water has even been ceremonially poured into a well built on the orders of a generous 19th-century maharaja for the English villagers of Stoke Row, near Reading.

Reverence for the river should come as no surprise. Descending rapidly from the Himalayas before winding across its fertile and densely populated floodplain in north India and Bangladesh, the Ganges has helped to sustain a tenth or more of the world’s population with food, water and fish for millennia.

Like many non-Indians, I was vaguely aware of the sanctity and the economic and social importance of the river before I came to live in India three years ago. In his famous travel book Slowly Down the Ganges (1966), Eric Newby lists translations for 108 of the sacred Sanskrit names for the river, among them “eternally pure” and “a light amid the darkness of ignorance”. Legend has it that Shiva protected the world from Ganga’s destructive power when the cosmic waters fell to earth by releasing the streams gently through his hair. One Sanskrit hymn calls the river the “sublime wine of immortality”.

What I had not expected was to find the Ganges so polluted by untreated sewage, industrial waste and pesticides that parts of the river and its tributaries are not only filthy and unsightly but disease-bearing, toxic and carcinogenic.

The crisis afflicting their emblematic river has not escaped Indians themselves. Narendra Modi, the Hindu nationalist leader who swept to power in last year’s election, abandoned his constituency back home in Gujarat and chose the ancient city of Varanasi (Benares) on the Ganges as his parliamentary seat. He called the river his mother and promised a clean-up. Hundreds of millions of dollars worth of projects since the 1980s have failed in this aim, and when Modi met President Barack Obama for an informal White House dinner last September, the talk turned almost immediately to climate change and the new effort to clean the polluted Ganges. Obama told Modi that the river in his native Chicago, once so filthy it used to catch fire, was now a place where fish were caught and eaten. “That’s exactly what I want for the Ganga,” said Modi.

By then — piqued by 1970s photographs showing weekend dinghy sailing in Delhi on a Ganges tributary that is now a fetid open sewer — I had already made it a mission to discover what ailed the river and why, and had decided to see as much of it as I could from source to mouth. Good scientific data, especially on industrial pollution, are scarce in India. But the conclusions of official measurements, academic papers and the evidence of one’s own eyes are alarming for anyone who cares about human health or the environment.

Delhi’s Yamuna River, one of the great tributaries of the Ganges, is a good place to start. Portrayed in Indian legend as a natural paradise of lilies, turtles and fish enjoyed by the flute-playing Krishna and his adoring gopis, almost all its waters are now diverted above the capital for irrigation. In the dry season before the monsoon, what flows from greater Delhi’s 25 million inhabitants towards Agra and the Taj Mahal is a toxic mixture of sewage and industrial waste, foaming hideously into windblown heaps of spume as it passes the Okhla barrage.

First, the sewage. At its worst — according to the 2011 water quality statistics published by the Central Pollution Control Board (CPCB) — the Yamuna’s water at Okhla contains 1.1 billion faecal coliform bacteria per 100ml, nearly half-a-million times the (Indian) recommended bathing limit of 2,500. The reason is clear. Half of India’s 1.3 billion inhabitants lack toilets; if they have them, they may not be connected to drains; if they are, there may be no sewage treatment plant; and if there is, it may not be working. The CPCB says only a tenth of the sewage produced along the main stream of the Ganges is treated at all. It is small wonder that those who can afford it use high-tech water filters to ensure the cleanliness of their drinking water, or that more than 300,000 Indian children under five die each year from diarrhoea, many of them in the Ganges basin.

2,500km Length of the Ganges; starts in Gaumukh, Himalayas and ends in the Bay of Bengal

Equally sinister are the findings of scientists investigating the rapid, sewage-borne spread of genes known as NDM-1 and NDM-4 (NDM stands for New Delhi metallo-beta-lactamase) that associate themselves with bacteria to form ­“superbugs” highly resistant to most kinds of antibiotics. NDM-1 was first detected in Delhi drinking water in 2010, and David Graham, a Canadian environmental engineering professor at Newcastle University, told me that he, as a visitor to India, and I, as a resident of Delhi, were both likely to be harbouring NDM-1 in our guts. A research paper he co-authored last year found that concentrations of NDM-1 in the relatively clean waters of the upper Ganges multiplied greatly when Hindu pilgrims from India’s big cities visited holy sites such as Rishikesh and Haridwar in the early summer. The rise was correlated with increases in faecal bacteria, too, suggesting that poor sanitation was once again the cause of the contamination. It is a grim irony that urban Indians who come to pay homage to the Ganges end up dirtying the river and spreading exposure to life-threatening diseases across the country.

The second problem is industry. A recent sampling of the Yamuna’s sediments, where many of the capital’s vegetables are grown when the river is not in spate, found the riverbed to be “highly contaminated” with carcinogenic and poisonous heavy metals, including lead, cadmium, chromium, mercury and arsenic — all except the naturally occurring arsenic being largely the product of India’s rapid industrialisation. “This is alarming,” says Prashant Rajankar of Toxics Link, the environmental group that published the study. He adds that more research is needed now into the vegetables themselves. Even for the main stem of the Ganges, there is little information about the scale of the crisis. The CPCB merely mentions 764 “grossly polluting industries” and says how much wastewater they produce — but not what is in it.

. . .

One obvious way to grasp the effects of human waste and industrial toxins is to compare locations upstream and downstream. So, with the help of the World Wide Fund for Nature (WWF), I visited stretches of another important Ganges tributary, the Ram Ganga. The contrast was startling.

32,000 corpses Are cremated in Varanasi each year and 200 tonnes of half-burnt flesh end up in the Ganges

In the hills near Marchula, the Ram Ganga flows clear and fast, home to fish eagles and otters. Stand on the bank and you can see golden and silver mahseer fish swimming in the pools and hear the harsh bark of the sambar, a type of deer, from among the trees. Anil Kumar, a guide and ornithologist from the village of Bakhroti, perched high on a hillside, points to tiger footprints, the dung of wild elephants and a pool where he caught a 68kg catfish two years ago. I jump in for a swim and wash off the grime of the long journey by car and on foot from Delhi. In a village above the river, Basanti Devi — who thinks she might be about 50 years old — complains that wildlife is too abundant, with elephants destroying the vegetable crops and tigers occasionally eating a cow. “I saw a tiger right here two months back,” she says.

The descent to the plains of Uttar Pradesh (at 200 million, the state has as many inhabitants as Brazil) is a shock. By Indian standards, Moradabad is not a particularly large city — just one million people — but there is no sewage treatment and there are scores of paper mills, sugar plants, brass foundries and plastics factories nearby that spew waste into the Ram Ganga and its tributaries. Downstream of the city centre, the sandy banks and the exposed riverbed present an apocalyptic scene of filth and garbage, of dead dogs, plastic bags, nullahs (drains) spewing pink dye and pigs rootling through the muck. All the while, men with tractors and bullock carts are mining sand for construction, while dhobi-wallahs (washermen) ply their trade in the dirty water and a boy forlornly casts his net for fish. In the Lal Bagh district, men and women squat in the shallows swirling the waste ash from the foundries in deep bowls to recover tiny remnants of metal. We had been told that the panning of incinerated electronic waste is done here at the dead of night — it is illegal because of the known toxicity of many of the components — but at least one boy is openly panning his e-waste in the daylight to extract wire and other valuables.

“When I was young this river was very clean and we could even see the riverbed,” says Mairaj Uddin, a Moradabad dentist who has become a Ram Ganga Mitra (crusader), one of a group of anti-pollution volunteers formed by WWF-India. As he speaks, someone hurls a plastic bag of rubbish from the walls of the nearby Ganga Mandir, a Hindu temple, straight into the river. “Now it’s dead. All the sewage from the city comes into the river. But things should change once the sewer line is laid . . . And I really hope that I’m going to help make this river go back to its original state. Maybe I’ll be too old to bathe in it. But I want my children to bathe in it.”

The same pattern — cleaner water upstream, filth downstream (faecal contamination is “off the charts, ridiculously high”, says one World Bank official) — is repeated around all the great pilgrimage sites and cities along the Ganges.

Near the Hastinapur wildlife sanctuary, between Haridwar and Kanpur, it is almost possible to imagine what the Ganges was like in its stately progress across the north Indian plains before the industrial revolution, the building of dams and the population explosion. We encounter a cheerful crowd of pilgrims, waving flags, blowing trumpets and carrying brass pots of river water as they return from their prayers to Ma Ganga. Ducks and waders feed in the shallows while river turtles and endangered gharials, the thin-snouted crocodiles of the Indian subcontinent, bask on the sandbanks.

There is an obstacle to change: so sacred is the Ganges that she is considered beyond harm

The industrial town of Kanpur is another story. So vile is the effluent from its 400 tanneries — including dyes, salts, acids and chromium compounds — that the government temporarily shut them down for the 2013 Kumbh Mela downstream in Allahabad. I was among the tens of millions who bathed in the Ganges at this Hindu festival, reputed to be the largest gathering of humans on earth. Rakesh Jaiswal, a Kanpur environmentalist, calls the tannery waste a “toxic cocktail” of chemicals that afflicts farmers using the water with rashes, boils and numbness in the limbs. A few years back he helped the Blacksmith Institute, a non-profit group that tackles pollution, to protect a Kanpur community of 30,000 from hexavalent chromium — Cr (VI) — in their groundwater. Known to cause lung cancer, liver failure and premature dementia, Cr (VI) had been found at a concentration more than 100 times the Indian government limit.

Move still further downstream and you reach Varanasi. I assume that this — the cultural heart of India and of Hinduism and, it is said, the world’s oldest living city — must be the place to understand what is being done to the Ganges and why Indians so abuse the river they worship. At dawn near the ghats (the riverside steps) and funeral pyres, holy men meditate and pilgrims bathe. A pair of dogs fight over charred human remains on the muddy shore (one scientist has calculated that 32,000 human corpses are cremated here each year, with 200 tonnes of half-burnt human flesh discharged into the Ganges). The rotting remains of a monkey, its face distorted in a watery rictus, is caught on a boat’s mooring line. A rotund man snorts like a hippo­potamus as he swims across to the far bank and a yoga lesson broadcast by loudspeaker punctuates the subdued roar of awakened humanity.

Even here, in a seat of ancient learning and religion, there is little scientific data on the Ganges, but the anecdotal evidence and the facts that do exist are scarcely comforting. Atul Gawande, the Indian-American surgeon and writer, describes in Being Mortal — his book on ageing and death — how he came to Varanasi to commit his father’s ashes to the Ganges. Knowing both the ritual and the unhygienic state of the river, he carefully dosed himself with antibiotics, hoping to avoid illness from the three spoonfuls of bacteria-filled river water he would be made to drink by the pandit presiding over the ceremony. Instead, he caught Giardia, a parasitic infection resistant to the antibiotics.

Few residents are aware of such dangers, and even if they are, they are unsure what to do about them. “I still bathe in the river on major Hindu festivals because that’s what everybody here does,” says Rina Verma, a 17-year-old student who lives at nearby Assi Ghat. “I feel really offended when outsiders come here and say they will not touch the river because the water’s very dirty,” she adds. Some locals say they learnt to swim in the Ganges but have now stopped and keep their children away. “My son asks me, ‘You all had so much fun in your time going to the river, what about us?’” says Govind Sharma, a small trader of 43 with a 10-year-old son. “I have no answer. I feel sad and guilty.”

When I was young this river was clean and we could see the riverbed. Now it’s dead

As in the Yamuna, the pollution is not just from sewage. Scientists Anand Singh and Jitendra Pandey at the city’s Banaras Hindu University (BHU) last year published one of the first detailed studies of heavy metals in the Ganges. They found concentrations increasing steadily as they moved downstream past Varanasi, suggesting that its own waste was the main contributor. After the city, concentrations of both lead and cadmium were typically about three times the World Health Organisation’s “maximum admissible concentrations”. Noting the resultant risk of everything from birth defects to cancer, Pandey said the presence of the toxic metals was “a health concern directly to human beings”.

It has been known for years that there are alarmingly high rates of certain cancers in the Gangetic Plain. Women in Delhi show the highest rates of gall bladder cancer in the world. Indian scientists hesitate to say which heavy metals, if any, are the cause, although a preliminary Indo-Japanese joint study in 2012 found “significantly high” levels of chromium, lead, arsenic and zinc in the cancerous gall bladder tissues of Indian samples when compared with those of Japanese sufferers.

. . .

So why allow the pollution, then? It is not just that people are oblivious to the ugliness or ignorant of the dangers; that was true of most countries during their industrial revolutions and is changing fast. In India, there is an additional obstacle to change: so sacred is the Ganges that she is considered beyond harm. Her waters are pure, medicinal even, and she is the responsibility of the gods, not of humans.

Ilija Trojanow, the Bulgarian-German author of Along the Ganges, encountered this phenomenon more than a decade ago. On the Ganges in Varanasi, he observed “yellowish foam that stinks worse than a rotting carcase, boils of pus on the holy body” but found that true believers would not acknowledge the sacrilege or accept the warnings of environmentalists. “They love Ganga mata-ji [Mother Ganges], and their love does not permit them to speak ill of her.” Varanasi environmental scientist BD Tripathi tells me his mother and other devotees were appalled when he started measuring the pollution 40 years ago. “They said: ‘You are not a Hindu. The water of Ganga is the most pure.’”

Tripathi has not given up, and hopes Modi’s plans — including sewage treatment plants, the deployment of 40 “eco-battalions” of soldiers and a project to make the river navigable again from the sea all the way to Kanpur — will achieve more than the lethargically pursued efforts of the past. “Why protect the Ganga?” asks Tripathi. “It’s a question of survival, the survival of 450 million people. It’s not religious sentiment . . . Ganga is a life-support system. It provides water, it provides nutrients, it enhances fertility of soil in the basin.”

Later I meet Vishwambhar Nath Mishra, a mahant or high priest, as he holds court at the Sankat Mochan temple to Hanuman the monkey god in the heart of Varanasi. The temple is like a busy medieval cathedral but the mahant is anything but medieval. He is a professor of electronics engineering, heads a foundation to protect the Ganges and has an intimate understanding of sewage treatment and political will: both, he says, are sorely lacking when it comes to the Ganges. “We are actually expert in complicating a problem and not finding a solution,” says Mishra, who is proud to have extracted a pre-election promise from Modi at the temple to save the river.

Like Mishra, I found the plight of the Ganges to be no mystery as I travelled along its length. It can be saved just as the Rhine and the Thames were [see below]. “We need to bring a transformation in our country,” says Vinod Tare, an environmental engineer from Kanpur who leads an effort by the elite Indian Institutes of Technology to research and restore the Ganges. “The government is very serious — no doubt about it. But the problem is so huge, it’s not going to change overnight. The Thames took 20 or 30 years and the Ganga is much bigger, so it’s going to take time.”

People are not the only victims of pollution. My next stop after Varanasi is Patna, a metropolis the size of Rome where I am astonished to see endangered Gangetic dolphins in the river in the city centre. It is good news that the dolphin, called the water-hog by the Mughal emperor Babur and known as susu for the breathy noise it makes on surfacing, is able to coexist with humanity, although I am saddened to find them fishing amid the garbage of what smells like a sewer outfall and to hear that they are repositories of organochlorine pesticide residues. Nearby, a partly burnt human corpse caught on some underwater obstruction twists in the current, jet-skiers amuse themselves by roaring in circles, and dogs gnaw at the ribcage of a dead cow.

After Kolkata — formerly Calcutta, the old capital of the British Raj and the last great city, along with Dhaka in neighbouring Bangladesh, to pour its filth into the Ganges — the journey down India’s sacred river draws to a close. In its parting gift to the land, the river spews millions of tonnes of fertile silt on to the rice fields and mangrove swamps of the Sunderbans at the Ganges delta.

On the far side of India from Gaumukh and with the air 35C warmer, boat skipper Tapan Das is as much in awe of the Ganges at its mouth as Amod Panwar was at its source. Two years ago, Panwar’s new hotel on the upper reaches was left teetering on the bank when the river tore out a new course after a monsoon cloudburst that swept 6,000 pilgrims to their deaths. Das was just nine when his father drowned in a storm on the delta, leaving him to support his four younger siblings, and he recalls the destruction wrought by Cyclone Aila in 2009.

Panwar and Das will welcome any action to mitigate climate change, protect the Ganges watershed and cleanse its waters of the waste that exposes them and their families to the risk of death by disease. What is not clear, however, is whether such Indians in their twenties and thirties will live long enough to see the benefits of the enormous clean-up task announced but barely begun by Modi. As Harvard’s Diana Eck has written, a river seen as a source of salvation by the millions who include it in their daily rituals is now itself in need of saving. The issue is not just environmental, “it is a cultural and theological crisis”.

Even the secular Jawaharlal Nehru, first prime minister of India, asked for his ashes to be thrown in the Ganges, which he called “a symbol of India’s age-long culture and civilisation, ever-changing, ever flowing, and yet ever the same Ganga”.

Das is no philosopher, but he knows the vagaries of the river as well as anyone. He points to a spot where he watched a Bengal tiger on a mudbank a month ago. “Storms and cyclones are happening more often than before,” he says as silt surges from the depths in thick brown eddies of warm water around the boat. “The current is faster and stronger.” Ahead of him, in the distance, the turbulent waters of the holy Ganges finally meet the Bay of Bengal and the open sea.

Victor Mallet is the FT’s south Asia bureau chief

Photographs: Poulomi Basu

Great river clean-ups

The Thames, 346km

In the 19th century, the Thames was so thick with sewage and industrial waste that cholera broke out and sittings of the Commons were abandoned because of the “Great Stink” of 1858. Today, fish and waterbirds have returned to the river. This was a subject of discussion between Nick Clegg, UK deputy prime minister, and Narendra Modi when they met last year. Clegg commented afterwards: “Cleaning up the Ganges is of course a challenge on a much, much bigger scale.”

The Rhine, 1,232km

The World Bank’s India chief, Onno Rühl, who is helping oversee $1bn of planned aid to clean up the Ganges, compares the task to that of restoring the Rhine in the 1980s. “It cost about €40bn to get to a sustainable outcome,” said Rühl. “You would not expect cleaning the Ganges to be cheaper than cleaning the Rhine was.”

The Chicago River, 251km

When Narendra Modi discussed environmental issues at the White House last year, Barack Obama told him that the river in his native Chicago, once prone to fires as a result of oil residues and other filth, was now so clean that you could eat its fish.