On a sunny autumn morning in London's financial district, Rod Guzman is looking for his favourite seal. Right next to the banking hub of Canary Wharf, between the grimy docks that once formed a global shipping port, lies a hidden hotspot for herons, cormorants, moorhen – and seals.

"When I do this, it usually comes," says Guzman, who works at the Billingsgate fish market next door, as he kicks a metal rail with his heavy boot, producing a deafening clanging sound. "I think it can feel the vibrations in the water. It's massive. Some give it names, like Alfred. I just call it the seal."

More than 2,000 seals have been spotted in the Thames over the past decade, according to a survey by the Zoological Society of London that ran from 2004 to 2014 and was published in August 2015, along with hundreds of porpoises and dolphins and even the odd stray whale.

Even though other problems now are threatening the health of the river and its animals – namely, its abundance of plastic – that's a big change for a river once so polluted, not even fish could survive in it.

In 1957, the Natural History Museum declared the Thames biologically dead. News reports from that era describe it as a vast, foul-smelling drain.

A member of the House of Lords was reported as saying purifying the river was unnecessary

"The tidal reaches of the Thames constitute a badly managed open sewer," the Guardian, then called the Manchester Guardian, reported in 1959. "No oxygen is to be found in it for several miles above and below London Bridge."

Wartime bombings had destroyed some of the old Victorian sewers that previously helped keep the river clean. Post-war Britain did not have the resources – or, it seems, the energy – to fix the problem quickly.

In another Guardian article from 1959, a member of the House of Lords was reported as saying purifying the river was unnecessary: rivers were "natural channels for the disposal of waste," and letting them break up organic waste gave them "something to do."

But although bacteria help rivers break down sewage, they use up oxygen in the process – potentially leaving none for other life forms.

It was only from the late 1960s onwards, when London's sewage system gradually improved along with the country's wider post-war recovery, that the river began to breathe again.

There are now 125 species of fish in the Thames, up from almost none in the 1950s

Other factors played a role in the clean-up, too. In the 1970s and 1980s, as part of a general increase in environmental awareness, concerns grew over the pesticides and fertilisers that were washed into Britain's rivers with every rainfall. Tighter regulations followed, says Chris Coode, the deputy chief executive of Thames21, a charity dedicated to improving London's waterways.

Other trends are more complex. For example, pollution from toxic metals in the river has dropped since the early 2000s, according to David Morritt, an expert in aquatic ecology at Royal Holloway, University of London in Egham, Surrey, UK. While partly due to stricter industry regulations, in the case of silver – a common pollutant from the photographic industry – the change was simply the result of people switching to digital photography.

Whatever the reasons, the result has been clear: the fish came back. There are now 125 species of fish in the Thames, up from almost none in the 1950s.

"You make the river as natural as possible, with clean water and proper flows, and then you'll see the community return," says Coode. "This wasn't about people breeding species in captivity and releasing them. The fish returned naturally."

The Thames is definitely cleaner that it was

The fish in turn feed marine mammals, including seals. While the public's attention tends to be on the playful seals and porpoises – what conservationists call "charismatic megafauna" – Coode is more excited about the return of a somewhat less photogenic species: sea lampreys.

"They're ancient, jawless, eel-like creatures that latch onto the sides of larger fish and suck their juices out," he says, with genuine enthusiasm. "They are very sensitive to pollution."

But while some threats have receded, others have emerged.

"The Thames is definitely cleaner that it was," says Morritt. "But there's a new kid on the block that we've become aware of, and that's plastic."

The central London section of the Thames is hemmed in by high walls and teeming with passenger boats

In 2015, one Royal Holloway study found that up to 70% of flounder in the Thames had bits of plastic in their guts.

The plastic can affect large animals, like the much-written-about albatross chicks that were fed plastic by their parents. But it also affects smaller creatures that are prey for the bigger ones. When they become ill, so do their predators. That finding has not yet been published and is currently under review with a journal, Morritt says.

The Cleaner Thames campaign was launched in September 2015 to combat plastic waste. It's a difficult battle, because there are so many sources.

Small pieces of plastic, like the plastic sticks of cotton buds and microbeads from facial scrubs and toothpaste, are often flushed down the toilet or the sink. They can pass through the filters and screens in sewage treatment plants, and they take decades to decompose.

Sometimes I think it's like an oasis

Meanwhile, plastic bags and thin plastic cigarette wrappers, even if properly disposed, can enter the drains by blowing or spilling out of overstuffed public bins. Thames Water, a private utility company in charge of London's water supply and waste water, says it removes more than 25,000 tonnes of debris from their sewage system every year.

The Thames wildlife revival faces other limits.

For example, the central London section of the Thames is hemmed in by high walls and teeming with passenger boats. That means it is too noisy, crowded and fast-flowing for porpoises or dolphins to ever swim upstream in great numbers, Coode says. Seals stand a better chance because they don't rely on sound for hunting, making them more resistant to noise.

Even the sewage problem has not been completely solved. Heavy rainfall typically overburdens London's creaking sewers, and the excess – rainwater mixed with sewage – is discharged into the river to prevent floods in the city.

Coode hopes that the planned Thames Tideway Tunnel, a major new sewer, will provide relief. Construction is expected to start in 2016.

Regardless of the problems, for Guzman the river's beauty outweighs the grime. He and his colleagues relax after early-morning shifts by feeding the seal. They give it salmon heads and other market scraps.

The animal has become a Billingsgate mascot

Munching on a chocolate bar as he waits, Guzman points at some ducks and other birds resting on a crumbling concrete pier. "Sometimes I think it's like an oasis," he says. "I take my break over there, enjoy the sun and just start looking."

The market has closed for the day. Guzman tries one last time to attract the seal by banging on the metal rail. The animal has become a Billingsgate mascot, written up in newspapers and even appearing on the BBC. But today, it seems to have other plans.

Guzman isn't perturbed. He takes one last look at a couple of birds basking in the autumn sun, against a backdrop of steel-and-glass skyscrapers. "It's amazing to think we have wildlife here," he says.

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