“That one is definitely over five years old, it could be eight to 10 years old,” shouts Dr Peter Walker, as a writhing 50cm long eel is scooped out of the River Tone near Taunton in Somerset. “This year or next I would expect this one to be on its merry way.”

The European eel makes an extraordinary 6,000km (3,728-mile) journey to the Sargasso Sea in the north Atlantic to spawn, from where its larvae travel all the way back. Now scientists hope a new project may shed light on this still mysterious part of eels’ lifecycle, which could provide crucial help in protecting the species.

Once plentiful, European eel numbers have plummeted in recent decades and it is now critically endangered, making it more at risk of extinction than giant pandas or elephants.

On the tree-fringed river bank, sunlight filters through the leaves and reveals the captured eel’s dark green sheen and pale belly and its narrow, dragon-like head. Eels like this need urgent protection and Walker, the lead aquatic ecologist at RSK consultants, is leading a project to identify the best habitats.

Aquatic ecologists Nick Monaco, right and Dr Peter Walker conduct an ‘electrofishing survey’ in the River Tone. Photograph: Jim Wileman/The Guardian

Trying to measure the squirming eel’s length, Nick Monaco, another RSK ecologist, says: “They are so slippery – as you’d expect. So eel measurements are always a bit approximate, shall we say.” The muscly creatures feel like a wriggling bar of soap, but this one stretches to half a metre, the longest of the day.

“Eels like to rest up in little hidey-holes and go out and forage at night,” Walker says. “The good habitat is on the margins – fallen trees and roots are perfect, so this is a good site.”

Boulders, undercut banks and dense aquatic plants also provide shelter and the team have surveyed 16 sites in England as part of the two-year project funded by the Environment Agency. The eels, along with some minnows and mayfly larvae, are captured by electrofishing, where a small current is used to briefly stun the creatures. The battery backpack and long pole ending in a metal loop look like something from Ghostbusters, but require great skill to use.

Dr Peter Walker takes the measurements of a specimen found in the River Tone. Photograph: Jim Wileman/The Guardian

The project findings will be used to help place measures to protect the eels in the optimum sites. The measures include the screens on water inlets at power plants and ladders that skirt weirs. It is thought that eels once made up about half of all the fish in British rivers by weight. “It is very sad we are at the stage where they are critically endangered – the next stage is extinction,” says Walker. “We can’t ever let it get to that stage.”

The exact combination of causes that has led to the crash in eel populations is not known – pollution, dams and climate change are all probable factors. While limited commercial catches are still permitted, poaching is also a serious problem.

Europol estimate that 100 tonnes a year are smuggled to China for consumption, earning criminals many millions and possibly billions of euros. In April, Jean-Michel Zammite, the police director of the French Agency for Biodiversity, said: “It sometimes can pay as much as drug trafficking.” The EU banned all exports of eels in 2010, but in late 2018 the European commission began a consultation on even tougher rules, saying that reproduction rates were at “an all-time low”.

Nick Monaco continues the electrofishing survey on the Tone. Photograph: Jim Wileman/The Guardian

Eels are also vital as fat-rich food for other wildlife and are eaten by pike, perch, trout and birds including herons, cormorants and bitterns. “They are a real favourite of otters too,” says Walker. “Trout in midstream are hard to catch, but eels sit under rocks thinking they are safe. But the otter uses its whiskers and snaffles them out – a high-calorie snack.”

Graeme Storey, an Environment Agency fisheries manager, says: “The EA is working hard to help in the recovery of our eel populations. We hope our use of the latest technology – from underwater cameras and electrofishing to detecting the presence of eels with environmental DNA – will play a major part in helping the eel and the diverse wildlife living in our waterways.”

Reviving eel populations is made harder by their lifecycle. Their transparent, leaf-like larvae transform into tubular glass eels as they approach European coasts, then as they push upriver they metamorphose into juveniles called elvers. They then grow into greeny-yellow adults and about a decade later turn silver and their eyes bulge as they reach full sexual maturity and head back out to sea.

In December, the EA and partners launched an attempt to solve the biggest enduring mystery – exactly where in the western north Atlantic eels go to spawn. Three eels big enough to carry satellites tags were released from the Azores, a staging post on their migration from Europe. The tags will release themselves in July and send back their data by satellite.

Reviving eel population is made harder by their life cycle. Photograph: Jim Wileman/The Guardian

The EA project leader Ros Wright said: “We hope that at least one of these three satellite-tagged eels will become a superhero to the species by completing the migration lifecycle, giving conservationists around the world the clues needed to protect this iconic species.”

Back by the Tone, Walker says he is optimistic conservation efforts will succeed in avoiding eel extinction: “They are very adaptable and hardy. If you give them an inch I think they will take a mile.”