Ali Sher Khan stands precariously on a piece of broken road that once led to the land where he lived before it was torn apart by the flood. The road has been replaced by a deep lake. Mr Khan, a clan leader in Rajanpur District in south Punjab, points grimly to the other side of the water where we can just see ruins of 200 houses where he and other members of his clan used to live.

A few people are trying to return to their house by driving a motor scooter, piled high with clothes, along a narrow path which skirts the newly formed lake. Mr Khan said that he and his neighbours lost their livestock and their possessions when water 15ft high surged through their settlement of scattered houses.

It is not the material losses alone that are worrying him. "Our people are dying because they have nothing to drink but dirty water," he said. Though half the land around is flooded, the water is brown, polluted by human and animal waste. "Even when we drill wells 50ft into the subsoil, the water is still filthy," he added.

As floodwaters recede across Pakistan, millions of people who survived the deluge are finding that they have nowhere to live and their fields have turned into swamps and lakes. For many of them, the worst is not over. The lack of clean water, as well as poor food, sleeping in the open and the collapse of any healthcare provision means the very young, the elderly and the weak are starting to die off.

The disaster that hit Pakistan in August when the Indus River turned into a 50km-wide torrent has faded from the headlines. But the effects are likely to kill far more people over the next few months than the 1,800 who died during the flood.

Many farmers – 80 per cent of the flood victims – escaped the rising water by taking refuge on higher ground. As they return to their villages, they are discovering that the sheer scale of the destruction is making it difficult to survive.

Mr Khan is not alone in finding that the floods have effectively poisoned the water above and below the surface. Other farmers across a wide area told the same stories of sickness and a mounting number of deaths. "Everybody affected by the flood is falling sick because we have no clean water, tents or bedding," said one man who is part of crowd desperately seeking aid from a local official. None of the victims of the flood appeared angry or raised their voices, perhaps still in shock from what has happened to them.

A second and more serious wave of deaths as a result of diarrhoea, malaria, cholera and measles in the aftermath of the flooding is predicted by the World Health Organisation and other UN agencies. The stagnant water is also an ideal breeding place for mosquitoes, which spread malaria. As many as 40,000 people are at risk of dying from the disease over the next four months.

People in Rajanpur know the danger of polluted water but in the moist heat of late summer in south Punjab they have little choice but to drink it. Everywhere we went in Rajanpur, there were children drinking and playing in the murky ponds. In desperation, some parents ask holy men to say prayers and recite verses from the Koran over buckets of dirty water, in the hope that their children can then drink it without getting sick.

But many people are beginning to lose hope and although sad-looking and malnourished farmers kept pressing their plastic identity cards into my hand, thinking I was an aid official who could do something for them, they did not look optimistic.

This part of Pakistan took the brunt of the flood because it is here that the five rivers, after which Punjab is named and which come from India, join the Indus. If this was not enough, the district straddling the Indus was also flooded from the west by torrents gushing out of the mountains that run north to the Afghan border. "We were hit by all the water flowing out of Afghanistan, India and Pakistan," says the local district officer Hussain Iqbal.

Such was the force of the flood that houses and villages were completely wiped out. And relief was even more inadequate than in other places because of Rajanpur's extreme isolation, 10 hours' drive from Lahore. "They suffer from the misery of those without power in Pakistan," said Shehryar Mazari, who farms 200 acres, as he watched hundreds of farmers looking in vain for help. Mr Mazari, who is intending to distribute 400 tents, is a senior member of the locally powerful Mazari tribe. Once a barrister and banker in New Zealand, he returned to Pakistan to become a farmer. He took us in his four-wheel drive as he assessed the damage in the sub-district of Sonmiani, on the east bank of the Indus, where he has his farm. It is one of the worst-hit places in Pakistan.

The force of the water from the flooded Indus did not just drown the land, it reshaped it. "I don't recognise what I am looking at," said Mr Mazari as he pointed out where the houses of friends had once stood and had now disappeared into the mud. Even buildings made out of modern brick have been smashed to pieces. Of the three main local crops – wheat, cotton and sugarcane – only the sugarcane has survived, while the cotton bushes have turned into a few shrivelled sticks and the wheat fields are often swamps. The mango trees are alive, though the leaves on their lower branches are shrivelled where they have been underwater.

We saw a tractor pulling a trailer loaded with women, children and household articles such as rope-beds disappear around a bend, presumably trying to go home. A few minutes later the tractor returned with its passengers, and when we drove further down the one-lane road, high on an embankment, we discovered why. The tarmac tapered into a track and then stopped abruptly: the land had disappeared. In its place was a newly created 12ft-high cliff at the bottom of which was a lake, 8ft deep.

We turned the car round and took another road that soon disappeared underwater for 200 yards. We got through because sticks or reeds had been stuck in the water marking where it was shallow enough to drive and a farmer waded in front to show us the way. We reached a cluster of tents where the road was blocked by a farm cart in which people were sleeping. A crowd of thin and ill-nourished men gathered and explained that they were fishermen on the Indus and of the 200 houses in their village, called Tutt, only two were still standing. During the worst of the flooding they took refuge in trees and only five had drowned: one man who had gone to look for his cattle and a second who had tried to escape on a motorcycle with his wife and two children. They were all swept away.

As in the other villages we visited in Sonmiani, the fisherman in Tutt said their younger children and the elderly were dying from dysentery and other illnesses because of drinking dirty water. Some aid had been delivered but had been taken by the better-off because those delivering it did not know who was most deprived. They agreed that they were catching more fish in the Indus, but fishing rights were owned by local notables and they could not fish without their permission.

The extent of the catastrophe has overwhelmed local administrations. Standing outside the wreckage of some farm offices in Sonmiani, the local revenue collector Mukhtar Khizar explained that out of 2,700 homes in his area, 500 remained. The army had handed out just 150 tents. People were sleeping on the ground and were getting ill from drinking dirty water. It was impossible to drill new water pipes through the mud, he said. There was a health clinic, but no doctor because he paid off officials to let him live in the town of Rajanpur on the other side of the Indus, and he never came near Sonmiani.

Mr Mazari's own house, which he built himself, was one of the few still standing. It has impressive towers at the entrance and the structure itself is still standing, though the interior was depressingly dark and dank. Mr Mazari was dismayed to find that all the olive trees he had planted had died along with 40 flowering trees he had ordered from all over the world. He said he is going to build a new house next to the old one.

On the other side of the Indus, the land is often semi- desert. Rojhan, the main town, is a mix of impoverished-looking shops and rubbish-filled streets. Low-lying parts of the desert have turned into lakes, while on drier ground people are taking advantage of the floods to sow sorghum. In Rojhan, the local 28-year-old member of the National Assembly in Islamabad, Mir Dost Muhammad Mazari, said that at one point during the floods the Indus was 50km wide, drowning much of his constituency; 84 out of 87 wards were badly damaged. He said that what people need most now is tents. "What I do is go out at night, and if I see a family sleeping on the ground I give them a tent if I have one."

The main government initiative is to give people 20,000 rupees (£280) to rebuild their houses, with more money promised later. Faith in government action is not high among Pakistanis, and the scale of the disaster would in any case stagger more robust administrations. Mr Iqbal, the district officer for Rajanpur, seems unfazed: "Our people are strong enough to absorb this kind of shock," he says, adding that by next year people will have planted a fresh crop of wheat and their lives will start to return to normal.

The destruction in Rajanpur is a snapshot of the situation facing at least six million Pakistanis who have lost everything. The floods have been described as "a creeping tsunami" but a better analogy to convey their terrible force might be a powerful volcanic explosion such as Krakatoa, which totally eliminated homes, crops and infrastructure.