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It may not look very inviting

William Blake wasn't using poetic licence when he wrote this first draft of "London" in 1792. Britain was at the height of the industrial revolution and the Thames had become a highway for commercial cargo. Meanwhile the capital's population used the river as a sewer, throwing in everything from raw sewage to their household rubbish. While the country was at the dawn of a new economic age, the Thames was being poisoned to death.

You may ask what's changed. To many Londoners, the river looks as grimy and forbidding now as when Blake described it more than 200 years ago. But this is a severe case of old ideas dying hard. Modern science is giving us a very different picture of Britain's greatest river. If Blake were to see it today, he would undoubtedly be in for a shock.

Despite its poor reputation, the Thames today is one of the cleanest rivers in the world: 120 species of fish swim between its banks and more than 400 species of invertebrates live in the water and on the shores. More than 200,000 wildfowl and waders spend their winters in the lower estuary. Even seals, porpoises and dolphins are making a comeback. The estuary is now one of the most diverse habitats in western Europe.

"This is a constant and steadily-developing recovery that's going on," says Steve Colclough, a fisheries expert at the Environment Agency. "If you look at the diversity of the ecosystem and use that as a reference to water quality, it's pretty good in comparison to most European estuaries." Blake's Thames, it seems, is just a distant and unpleasant memory.

Two hundred years ago there was no question that the river was in decline. The population of south-east England was expanding rapidly and factories were springing up all along the 300km- (185 mile-) long river, particularly near London. The introduction of the flushing toilet in the 1830s meant that raw sewage was pouring directly into the water and wreaking havoc on the wildlife. By the 1850s, central London stank so badly in the summer that parliament often had to be closed.

The lowest point came in 1957, when scientists declared the Thames biologically dead. The amount of oxygen dissolved in the river was so low that nothing could survive and the muds along the bank reeked of hydrogen sulphide.

It was at almost the same time that things started to change. "It was a combination of lack of industry, closing of the docks and people being much more concerned about how dreadful the quality of the river was," says Justin Dillon, chairman of London Wildlife Trust. The number of boats entering the river dropped with the decline of industry in the south-east. The government also spent money to improve sewage treatment works. With the sources of pollution under some control, the river started to heal.

"That's one of the beautiful things about estuaries - if you take the polluting loads off, they clean themselves very quickly indeed," says Colclough. "By the early 70s we were already starting to find fish and the number of species was up to 100 by 1980."

New species keep turning up. The 121st species of fish could well be the tompot blenney, an odd-looking orangey-brown fish normally found in shallow rocky waters, and seen for the first time in the Thames just a few weeks ago near Tilbury.

"Seals and harbour porpoises and dolphins are quite regular visitors now," adds Colclough. "There's a resident seal at the moment in Chiswick Reach, which is spotted almost daily. Dolphins and harbour porpoises tend to come up usually in the winter months."

Numbers have been growing for the past decade or so. Before then, these animals would have quickly died in the polluted river. As would the cormorants that fish between Blackfriars and Waterloo bridges every day, and the peregrine falcons, which can usually be seen near Tate Modern in Southwark.

To keep the animals (and us) safe from pollutants, the agency constantly monitors the water quality in the river. About 20 automatic monitoring stations stretching from Richmond in the west down to Purfleet in the estuary feed information about the physical and chemical status of the river 24 hours a day.

The things they measure include the amount of dissolved oxygen, the pH, presence of heavy metals, ammonia content, what suspended solids there are and biochemical oxygen demand. This last measurement gives an indi cation of how much organic waste is present in the water.

The monitoring stations help the agency react quickly to problems. If, for example, a stretch of water is found to be low in dissolved oxygen, the agency can dispatch "bubblers". These can inject up to 30 tonnes of oxygen into the water per day, thereby saving the animal population from suffocating. The end result of the monitoring is, simply, much cleaner water.

"[Thames water] is not something you'd like to necessarily take in great gulps of but it's much cleaner than the ordinary member of the public thinks," says Dillon.

Even swimming in the river, often thought of as a complete no-no by most people, is safe from a health perspective. There is a proviso. "Twice a day, a huge amount of water floods in and floods out and it goes very quickly so there's a very strong undercurrent," says Dillon. "It's amazing how many people drown each year through falling in and not realising how strong the current is."

At its greatest, the drop between high and low tide is 8m. Most rivers are nowhere near as tidal, but this constant charging backwards and forwards of the water has its uses: it not only dilutes pollution, but also promotes life in the river. The mixture of salt and fresh water, for example, brings sea fish such as anchovies, cod, eel, haddock and mackerel into the Thames.

Despite the diversity of the ecosystem and the proven cleanliness of the water, the stigma attached to the Thames is hard to shift. Partly it is due to the murky brown look of the water (caused by the muddy substrate in the river which, if settled out, would leave relatively clear water), and partly it is historic.

"People always thought of the Thames as being a dead river," says Dillon.

Several people are trying to reverse that image. As part of the mayor's Thames festival next month, for example, Dillon hopes to challenge public perceptions by talking about the environmental diversity in the river and leading the first science day in the history of the festival. Another group, the Thames Estuary Partnership (TEP), has started a project to pull together all the scientific work done on the Thames to try to re-educate people.

"What we try and do is provide an integrated look at how biodiversity and water quality interact," says Tim Chapple, executive director of the partnership. "There is quite a lot of data by individual organisations but there isn't is an overview."

For people engaged in research on the Thames, the TEP's work will set up benchmarks for the state of the river and will allow them to monitor future changes. For everyone else, the partnership intends to publish a book that it hopes will publicise the real story of today's Thames.

Dillon is confident that people will start to see the river in a whole new light one day soon. "It might have a murky past, but it's got a much cleaner present than it would seem on the surface," he says.

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