Thousands of English farmers may have to stop farming next to rivers, lakes and other water bodies in the biggest crackdown on agricultural pollution, which the Government will announce today.

Thousands of English farmers may have to stop farming next to rivers, lakes and other water bodies in the biggest crackdown on agricultural pollution, which the Government will announce today.

They will be caught in a tough new water quality regime that will aim to halt one of Britain's least visible but most serious environmental problems - the overloading of watercourses with fertilising chemicals washed off farmland.

The vast majority of England's 200,000 farmers will need to make significant changes to farming practice to comply with the new regime, such as altering the times at which their fertilisers are applied, or improving their drainage. But government officials believe that, in the most difficult cases where this is not sufficient - perhaps 10 to 15 per cent - farming in areas adjacent to water bodies will have to stop.

The problem of agricultural pollution has been increasing steadily since intensive farming got going 40 years ago. Scientists and wildlife campaigners have long claimed it is causing huge damage to plant and animal communities, often because of the resultant super-growth of harmful organisms such as algae.

Heavy loads of nutrients such as nitrates and phosphates, put on the land as fertilisers and subsequently washed off, have led to increasingly frequent "algal blooms", which are potentially poisonous and have caused lakes and reservoirs to be closed to the public. They have also upset the ecological balance of many rivers and reduced plant and insect life.

A report will describe in detail for the first time the damage done by agricultural pollution to water bodies, especially important aquatic wildlife sites, and a consultation document will invite opinions from the farming community and other interested parties on how best to tackle it.

Tackled it will have to be, not least because of a new and vigorous European water quality law being brought in over the next decade. The EU Water Framework Directive will, for the first time, demand "ecological" quality from all water bodies - meaning that they will have to be returned to something like their pristine natural state.

The Environment Agency is carrying out a massive survey of all water bodies in England and Wales to see how they fit in with this requirement, and government officials have been alarmed at the preliminary conclusion that most of them do not.

Another major driver for government action is the public commitment to return 95 per cent of Sites of Special Scientific Interest - the prime wildlife areas - to favourable status by 2010. Last December a report from English Nature, the conservation agency, showed that nearly half of them were in poor condition, and rivers were in the worst state of all. The 33 English rivers and streams scheduled as SSSIs had more than two-thirds of their area in poor condition, and this included stretches of some of the most prestigious and beautiful rivers, the chalk streams of the southern counties such as the Test, the Itchen and the Hampshire Avon.

There has been no detailed survey yet of what areas might be most radically affected, or their extent, but this is coming, because under the Water Framework Directive, detailed river basin management plans will have to be in place by 2009.

"This is a huge issue," said a government source. "We have invested billions on water quality improvement through sewage treatment works, but on agriculture pollution, virtually nothing."