The famous stretches of river failed to meet new European standards for water quality that judge not only the chemicals in the water but the health of fish stocks and level of wildlife.
Conservationists said the state of rivers made famous in literature reflects the wider problem of pollution and called on the Government to be more ambitious in their clean-up programme.
The Environment Agency has disclosed that just 26 per cent of the country's 6,000 rivers are judged to be a "good" ecological status under the EU rules.
The stretch of the Thames from Reading to Cookham, that inspired Kenneth Grahame to write Wind in the Willows, is not expected to be clean enough to meet the top standard until 2027, largely because of chemicals in the water caused by farming.
A tributary of the River Medway near Ashdown Forest in Kent, where Christopher Robin invented pooh-sticks and the world championships of the game is still held, has also failed to meet the standard.
The Taw and Torridge in Devon where Tarka the Otter once swam does not have healthy enough fish stocks and dairy farming has also caused a high level of chemicals in the water.
Other rivers famous in literature that are judged to be below standard are the Thames between Kingston and Oxford that appears in Three Men in a Boat by Jerome K Jerome and the Severn that inspired Spencer's Fairy Queen.
Ralph Underhill, of the Royal Society for the Protection of Birds, said the Government should be aiming to make all rivers in Britain as clean as possible in the next five years.
"These authors drew their inspiration from from the beauty and wildlife of some of Britain's most famous stretches of river," he said. "But they may not even have come up with these famous pieces of literature if the rivers were not teeming with life. Not many people are inspired by a polluted river."
However the a spokesman for the Environment Agency insisted Britain's rivers are cleaner than they have ever been.
“We’re keen that as much as possible is done to get the water environment in the best possible condition. We can only increase ambition where we are confident that others will play their role in delivering the real environmental benefits we all want to see. So we will working with farmers, water companies and groups such as the RSPB to get the best deal for our environment," he said.