Just a quarter of rivers in England and Wales are in good health - with only five in top condition, according to new figures.
The Environment Agency's annual assessment of waterways showed seven out of 10 English rivers and nine out of 10 Welsh rivers had either "very good" or "good" standards of biological and chemical water quality.
But under higher standards set down by the EU, which include examination of habitat provided for wildlife and the impact of pressures such as water abstraction, only 26% of rivers reached the required "high" or "good" condition.
Almost three quarters failed to make the grade under the new standards, with 117 waterways getting the worst rating possible.
But the Environment Agency said its annual General Quality Assessment (GQA) showed rivers in the two countries were the best they had been in more than a century - with chemical and biological water quality improving for the 19th year in a row.
Many animals - including salmon, eels and otters - were returning to once polluted waterways as a result of investment by water companies, action against polluters, changing farming practices and local projects, the EA said.
RSPB director of conservation Mark Avery said: "There is no doubt that the millions of pounds invested by the water industry over the past two decades has brought real improvements to our rivers and coasts. But these alarming figures really show just how far we have to go to tackle the problems faced by our rivers."
Four of the five "high" quality rivers are in Northumberland, Ridlees Burn, Barrow Burn catchment, River Till and Linhope Burn, and the fifth, the Caletwr, is in Conway, Wales.
The Environment Agency acknowledged that more needed to be done to meet the EU standards, and said it would be working to transform 9,000 miles of river by 2015.
Dr Paul Leinster, chief executive of the Environment Agency, said: "Our rivers are at their cleanest for over a century, which is why we are seeing the return of otters, eels and salmon to the Thames, Mersey and Tyne. But we need to go even further to meet the new EU measures for water quality. That is why we have plans to clean up 9,000 miles of river over the next five years."