The sun shines on clear river water running through a valley in the Cairngorms, bringing the stones on the river bed into colourful focus. Here and there are dark shadows, half-buried clusters of dull black shells, lined and gouged by decades of shifting water and gravel: the pearl mussels of the river Dee.

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The pearl mussel is one of the most ancient invertebrates on the planet, a freshwater shellfish that has helped to shape the history of Britain. One pearl mussel in every 1,000 or 5,000 – no one can be sure – lives up to its name and contains a lustred treasure. Julius Caesar’s biographer, Suetonius, cites a desire for pearls as one of the reasons why the Romans invaded Britain in 55BC.

But pearl hunting, pollution and habitat destruction have almost led to the mussel’s extinction. It has been illegal to pearl fish and to sell or buy a Scottish pearl since 1998, but their numbers remain perilously low. This week or the next, some of the remaining female mussels along all 86 miles of the Dee will spawn – all at once. On just one day a year, they release millions of tiny larvae, or glochidia, into the water.

The baby mussels face the most extraordinary odds – they have to latch on to the gills of a passing fish to survive. Roughly one in four million make it, fewer if the salmon and trout are in short supply. Which is why a remarkable project is under way to attempt to transform the Dee, restoring its natural course to improve the prospects of the pearl mussel.

On the Slugain, a tributary of the Dee near Braemar, a giant digger has arrived, part of the £3.5m Pearls in Peril habitat restoration project being undertaken by Scottish National Heritage (SNH). The plan is to break down artificial banks and barriers that over decades have been built to force rivers off farmland or away from housing. These constructions funnel the water into channels that flow faster and fill up more quickly – a flood risk for towns and roads downstream – and no longer have the meandering shallows, cascades and pools that suit the mussels and the fish they rely upon.

“Anything you can do for a mussel has an immediate knock-on effect, on the salmon, on the trout and on the river,” said Jackie Webley, the SNH project manager. “Reinstating the natural progress supports the resilience of the river and everything in it. You really have to let the river do what it wants to do. It becomes slower and shallower, helping the fish to have safer nursery spaces. It helps the mussels, it helps the land. It helps people.

Facebook Twitter Pinterest Pearl mussels are the barometer of the Dee’s health, says Jackie Webley of Scottish Natural Heritage. Photograph: Martin Hunter/The Observer

“The pearl mussel is the barometer of river water health; if they’re deteriorating, then so is the river. If we can get them to flourish once more, that will have an enormous impact. Each mussel is filtering 50 litres of water each day, and here in the Dee that’s good news for 200,000 people in Aberdeen drinking it.”

On the Slugain, 200 metres of boulders will be pulled out; in the Dee last year it was 30 old cars. “The river was blocked with corrugated metal and railway sleepers, but then behind it we were pulling out old cars. One was a Bedford van with cigarette butts still in the ashtray,” said Webley.

Digging out these banks will allow the river to regain its natural course, while hundreds of native trees are being planted, dotted along the banks, to provide shade for river creatures. “Climate change means we are seeing substantial rises in river water temperature, so the trees will not only stop soil erosion but cool the water down as it passes underneath their shade,” said Webley.

The effects of catastrophic flooding during last December’s Storm Frank can be seen all over the Cairngorms – shops remain closed due to water damage and bridges no longer cross water where the river shifted its course.

Last year’s salmon numbers were poor in the Dee, worrying the fishing and tourism industry, which rely on the river for a living, just as the pearl fishers once did.

Bill Abernathy, 91, made his living pearl fishing the rivers of north-west Scotland. He can tell a mussel that holds a pearl just by looking at it, and could extract it without damaging the mollusc, using skills learned from his father. “A good living it was too. You couldn’t get a better occupation, out in the fresh air, your own boss.”

For those whose livelihood was dependent on the mussel population’s rude health, commercial exploitation, poaching and pollution were their enemies too. “People did, and still do, try to poach them. They think they will make their fortune, but of course they won’t at all. They just cause terrible destruction,” said Abernathy.

In 1967 he found the world’s most perfect freshwater pearl – named Little Willie in his honour – but refused to sell it, instead striking a deal with a Perthshire jeweller to keep it on display. “There was a nominal sum but no, I wasn’t tempted to sell it. It’s part of the history of the country, money is only one thing. If you haven’t got your health you haven’t got anything.

“The mussels have survived for thousands of years,” added Abernathy. “It would be a terrible tragedy if they were to go extinct in my lifetime.”

However, interest in this neglected mollusc is likely to be rekindled this month with the publication of a novel by author Julia Stuart set in the pearl fishing communities. “I discovered Scottish river pearls while visiting a family friend in the Borders,” she said. “When I told her I’d just found a pearl while pearl diving in Bahrain, she showed me an old necklace of white pearls which she said had been found in Scottish river mussels. I was astounded. Like most people, I thought pearls could only be found in oysters.

“While it’s a shame that such a fascinating and endearing Scottish custom as pearl fishing had to be stopped, it is an imperative. Pearl mussels are critically endangered and pearl fishing caused the extinction of many important populations. Anyone who is thinking they’ll strike it rich is deluded and risks being prosecuted. They probably wouldn’t find a pearl for a start and, if by some miracle they did, they couldn’t sell it as it would be illegal to own it.”

The Last Pearl Fisher of Scotland, by Julia Stuart, is published on 25 August (Vintage, £7.99)