The government is already on course to miss its legally binding target of restoring 77% of England's waters to good ecological status by 2027 - a goal the environmental watchdog, the Office for Environmental Protection, has warned will be missed by a "considerable margin".
It's now investigating both the government and the Environment Agency over possible rule breaches.
Environment Secretary Angela Eagle said the figures "underline the need for wholesale change across the water sector".
She pointed to new laws the government has introduced to hold water companies to account and record investment. "We will drive forward a system that puts the public interest first," she said.
Much of the debate about the state of England's waters has centred on water companies and the sewage they release into rivers.
But campaigners and scientists also point to agriculture as an equally large source of pollution - one that attracts far less public attention.
Erica Popplewell, of the campaign group River Action, said some farming, particularly intensive poultry units - vast sheds housing hundreds of thousands of birds - were a growing threat to rivers such as the Wye and Severn.
"There's a lot of poo that comes out of the chickens," she said. "If it goes straight into a river, it causes eutrophication. The whole ecology of the river is damaged, and the river is dying." She called on the government to tackle sewage and farming "with the same urgency".
The National Farmers' Union of England and Wales has been approached for comment.
Other types of pollution affecting England's bodies of water, the Environment Agency pointed to, include petrol, garden pesticides and contaminated water running off roads picking up microplastics.
The Environment Agency stressed that this year's data could not be directly compared with 2019 because it had changed its methods.
In particular, it said the steep fall in the number of lakes ranked as good - down about half from 2019 - largely reflected a change in how its experts now assess them, rather than a genuine decline in their condition.
Its chair, Alan Lovell, acknowledged too many water bodies were "still not achieving the standards we want to see", adding that the agency was "transforming our enforcement work" with its largest ever workforce.
But Prof Penny Johnes, a leading water quality scientist at the University of Bristol, told BBC News the true picture was almost certainly worse than the classifications suggested.
The scheme was "not fit for purpose", she said, measuring too few pollutants too infrequently, and missing nitrogen and other substances scientists have long understood to be driving rivers' decline.
The findings come as much of England sits in official drought, with rivers running low and more than 20 million people facing hosepipe bans.
Lower flows can concentrate the very pollution the new data is designed to track, leaving fish and other aquatic life exposed to more dangerous levels.
Climate change is expected to bring drier and hotter summers which could further exacerbate this issue.
Asked directly whether England's waters were healthier than six or seven years ago, Prof Johnes said: "No, definitely not."
Every river and lake failed the test for chemical pollution.
The Environment Agency said this is because legacy substances, such as heavy metals from mining, take decades to break down, and some are building up.
But Prof Johnes said it was also a "failure to regulate effectively" the new chemicals entering rivers, from antibiotics to the "forever chemicals" known as PFAS - many not routinely monitored.
There are currently 23 enforcement notices against water companies requiring them to lower the levels of PFAS to reduce the danger to human health.
Water UK, which represents the water companies, has called for PFAS use to be banned to limit their build-up and reduce water treatment costs, but the chemicals are currently used in thousands of products, from school uniforms to medical devices.
It said it was spending record amounts of money on improving the country's waterways.
"Water companies are investing £22bn in environmental improvements by 2030. This will help to secure our water supplies, support economic growth and end sewage entering our rivers and seas."
The Environment Agency also noted that other European countries are doing even worse in terms of the good health of their waterways, with only 8% in Germany and just 1% in the Netherlands.
But Prof Johnes said such a comparison is misleading, because of varying methodologies across nations.
