It has been a highway, a sewer and was declared biologically dead in the 1950s but the River Thames is now a nursery for 138 baby seals, according to the first comprehensive count of pups.

Scientists from ZSL analysed photographs taken from a specially-chartered light aircraft to identify and count harbour seal pups, which rest on sandbanks and creeks around the Thames estuary, downstream from London, during the summer, shortly after they are born.

“We were thrilled to count 138 pups born in a single season,” said conservation biologist Thea Cox. “The seals would not be able to pup here at all without a reliable food source, so this demonstrates that the Thames ecosystem is thriving and shows just how far we have come since the river was declared biologically dead in the 1950s.”

The Thames is home to both grey seals and harbour seals, although only the latter breed there. The seals can feed on more than 120 species of fish in the river, including two species of shark, short-snouted seahorses and the European eel, which is critically endangered. Marine mammals spotted in the Thames include porpoises, dolphins and “Benny” the beluga whale.

Facebook Twitter Pinterest A seal pup in the Thames estuary. The Thames is home to both grey seals and harbour seals Photograph: Tony Thomas/ZSL

The river’s seal population has risen steadily since ZSL began its annual count in 2013. The most recent results, from 2017, recorded 1,104 harbour seals and 2,406 grey seals across the estuary.

It is not yet known if the numbers were due to resident seals having pups or adults moving in from other areas, such as eastern Scotland, where seal populations have been falling.

Anna Cucknell, who leads ZSL’s Thames conservation project, said: “The restored ‘Mother Thames’ – as we call her – is an essential nursery habitat. Harbour seal pups can swim within hours of birth which means they are well adapted to grow up in tidal estuaries, like the Thames. By the time the tide comes in they can swim away on it. Grey seals, on the other hand, take longer to be comfortable in the water, so breed elsewhere and come to the Thames later to feed.”

While the harbour seals breed in the outer estuary, a swath of low-lying coastline between Felixstowe to the north and Goodwin Sands, off Kent, to the south, they forage right through London to Richmond, and can move beyond weirs in pursuit of food.

Cucknell added: “The Thames is home to more than 20 fish species that use the Thames as a nursery habitat. Marine species such as sea bass and flounder use it right in the city – past the Houses of Parliament and up to Putney, before they head out to sea. Having a robust and healthy food web plays a huge part in supporting top predators such as seals.”

According to Cucknell, pollution including sewage is “still a challenge” in the Thames. Poor plumbing in some housing developments still results in untreated sewage flowing into the Thames. ZSL is running a citizen science project called Outfall Safaris, in which volunteers walk along often-hidden tributaries and help trace the source of this sewage pollution.

Facebook Twitter Pinterest While the harbour seals breed in the outer estuary, they forage right through London to Richmond, pictured. Photograph: Alamy Stock Photo

A study found up to 75% of flounder caught in the Thames estuary had micro-plastics in their stomachs. “What the knock-on effect of that is on larger predators such as seals is totally unknown at the moment,” said Cucknell.

The latest seal pup survey is from 2018. Scientists are still analysing thousands of photographs from the 2019 count. ZSL is also asking people to help count and monitor the Thames seal population by logging on to its camera traps surveying different Thames-side “haul-out” sites, and recording what seal species they see there.

Cucknell added: “For a long time, we had our back to the water and we haven’t seen it as habitat, it’s just been a waterway. We’re trying to change people’s perceptions. We call it London’s biggest wildlife secret. They see the brown water and think it is dirty and dead. We hope people will take inspiration from it, and ownership of it.”

The Thames: a brief history of brown

The name of the longest river flowing entirely in England may derive from “tamasa”, a Sanskrit word meaning “dark water”.

The Thames has always been brown, and will remain so even if one day it is entirely free of pollution.

The brown waters are caused by eight-metre tides that scour its muddy estuary. They are the source of much of its biodiversity: allowing plankton to survive which feed off nutrients in the water column and provide food for fish.

Sixty years ago, however, the Thames was toxic. “The tidal reaches of the Thames constitute a badly managed open sewer,” the Guardian reported in 1959. “No oxygen is to be found in it for several miles above and below London Bridge.”

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In 1957 the Natural History Museum declared the Thames to be biologically dead. The Victorian engineer Joseph Bazalgette’s brilliant sewer system, which saved London from the “great stink” of 1858, had been damaged during the second world war. Parts had fallen into disrepair. Heavy industry used the Thames as its free waste disposal service.

Not everyone was outraged. The Guardian reported in 1959 that a member of the House of Lords opined that cleaning the river was unnecessary: rivers were “natural channels for the disposal of waste” and allowing them to break up our waste gave them “something to do”.

Repairs to the sewers and tighter regulations, including to reduce fertilisers and pesticides from farmland draining into rivers, gradually cleaned up the Thames, as did broader economic changes. The decline of Thames-side industry removed pollution; toxic metals have reduced since 2000, helped by the switch to digital photography, which has reduced the photographic industry’s silver pollution.

A time-traveller from the 1950s visiting the hides at the London Wetland Centre (created from disused reservoirs in Barnes) would scarcely believe the great white egrets, kingfishers, hobbies and dragonflies that are testimony to a new, enriched urban ecosystem.

The Thames is more wildlife-friendly than it was, but it is not perfect. Salmon were reintroduced to the Thames, but this scheme seems to have failed. The inner Thames is too busy and noisy with boats for dolphins or porpoises to thrive (seals do not hunt using sound and so are more able to survive alongside water traffic).

A species as rare as a tiger still snakes through the capital – the endangered European eel – but it is in drastic decline. Like London’s citizens, the future prospects for this and many Thames species depend on the world beyond it.