When Sir John Betjeman went to Marlborough College in the early 1920s, it was, by and large, a miserable experience. The future poet laureate found solace, however, in the countryside and churches around the school.

On his walks he fell in love with the subtle, gentle pleasures of the Kennet, one of the finest chalk rivers in England, which rises near the world heritage site of Avebury in Wiltshire and flows into the Thames near Reading.

"The smell of trodden leaves beside the Kennet, On Sunday walks, with Swinburne in my brain," Betjeman wrote in his verse autobiography, Summoned by Bells. And again: "When trout waved lazy in the clear chalk streams, Glory was in me …"

The poet would have been deeply saddened by the current state of his favourite river. The Kennet, like many rivers in the south of England, is running dry, a victim of high demand for water and more than a year of below average rainfall.

In a debate on the water white paper in the Commons earlier this month, Richard Benyon, minister for environment, food and rural affairs and MP for Newbury, said: "The river Kennet flows through my constituency, and when I stood in it in Marlborough the other day, it was as dry as the carpet on which I am standing."

In November, officers from the Environment Agency rescued more than 100 fish, including brown trout and grayling, from the Kennet near Marlborough, when water levels subsided to just a few inches.

Fish farmer and Kennet river keeper John Hounslow was not so lucky. He awoke one morning to find that 3 tonnes of trout – £30,000 worth – had died overnight. "There had been a heavy leaf fall," he said, "and the water flow was too weak to shift it. The main problem is both the lack and the poor quality of the water.

"The sewage works upstream releases discharge into the water, which is not an issue when the flow is normal. But when levels are so low, although the water looks clean, it is not oxygenated enough. The fish quickly use up what oxygen there is and then that's it – they die."

The Kennet is not alone. In the Environment Agency's west Thames area, which covers parts of Wiltshire, Berkshire and Oxfordshire, the Kennet and five other rivers – the Coln, Evenlode, Thame, Ock and Thames – are described as "exceptionally low", which means the flow is around half or less of the normal rate.

The most obvious cause of the rivers' plight is lack of rain. According to the Environment Agency, 18 of the past 20 months in the area have had less than the average rainfall, while the year from October 2010 to October 2011 was the fourth driest in the last 90 years.

Chalk streams such as the Kennet are fed by aquifers, underground reservoirs that cover hundreds of square miles and that are filled by rainwater that soaks through the chalk soil during autumn and winter. The water that seeps out from the aquifers into the rivers is at a constant temperature and provides an ideal habitat for insects, plants, fish, crayfish, birds and mammals like the water vole and otter. Kenneth Grahame based his classic book The Wind in the Willows on the Thames, a chalk river that receives much of its water from the Kennet.

But if what local farmers and anglers are calling a drought continues, the future looks bleak. "What happens over the next few months will be critical," said Graham Scholey, conservation technical specialist for the Environment Agency. "October to March is the main recharge period. If we have a dry winter, low river flow will appear even earlier next year and there will be greater environmental stress." For "environmental stress", read dry rivers.

Lack of rainfall is not the only concern, however. Every day Thames Water, under licence from the Environment Agency, pumps more than four million gallons out of the Kennet to supply homes and businesses in a process known as abstraction. While a third of that amount is used locally and finds its way back into the river, two-thirds is pumped 12 miles north to supply the growing needs of Swindon, a town of around 200,000 people. This water is lost for ever to the Kennet.

"It's true – the Kennet's never been as low as it is now," said Richard Aylard, Thames Water's sustainability director. "We want everyone to use water more carefully," he added. "We're trying to explain to them that there is a very direct link between what comes out of their taps and what comes out of the river."

Along with the Itchen and the Test, both in Hampshire, the Kennet was once one of England's most sought-after rivers among anglers. The river is mentioned in Izaak Walton's The Compleat Angler, a seminal work published in 1653 on the art and spirit of fishing, while Frederic Halford, the founder of modern fly fishing, fished many beats along the Kennet in the late 19th and early 20th centuries.

While you can still see the odd trout "waving lazily", the chances are it will be of the farmed variety. "When I started here 32 years ago, 60% of the trout were wild fish," said Hounslow. "Now I reckon it's down to 10%. The whole of the upper river has been destroyed. The lack of water flow means that we've lost almost all the ranunculus weed that holds lots of invertebrates and produces cover for the fish. This is unprecedented."

Scientists, farmers, water companies – all are agreed that, unless there is more than one-and-a-half times the average winter rainfall, next year the Kennet will be even drier, probably much earlier in the year.

"This is a wake-up call," said campaigner Charlotte Hitchmough, a member of Action for the River Kennet. For her, the root of the problem lies in the licences that were granted to water authorities decades ago at a time when water was plentiful. "You cannot have unlimited cheap water and lovely, flowing rivers," she added.

Alan Crook, a retired telecoms engineer, is 80 and has lived in Marlborough all his life. He remembers swimming in the Kennet as a child: "There were hatches to control the flow of water for the mills," he said. "The water there was 10ft deep. We used to jump in from the bank and have a whale of a time. Now the river's so low that children could never do that. Those days are gone for good."