Illegal freshwater pearl mussel fishing has damaged populations of the species in Assynt "for decades", Scottish Natural Heritage (SNH) has said.
Three incidents of poaching have been detected on different rivers in the area of west Sutherland.
In the worst of the incidents, thousands of empty shells were found.
Freshwater pearl mussels, which are a protected species, are slow growing and SNH said it would take decades for the populations to recover.
Pearl fishing involves breaking open the mussel shell, which kills the creature, to look for pearls which very rarely form inside the mussel.
Investigators from the Riverwatch initiative, which forms part of the Life+ Pearls in Peril Project, uncovered the illegal fishing.
The scheme aims to raise awareness of the offences in the Lochinver area of Assynt.
Police Scotland is among the organisations that support the project.
Ch Insp Colin Gough, wildlife crime co-ordinator for the Highlands, said: "Protected by law, freshwater pearl mussels are a very important part of a river's habitat, with illegal pearl fishing having the potential to devastate their fragile populations.
"Police Scotland will continue to work in close partnership with the Pearls in Peril LIFE+ project by supporting their river patrols, investigating any reports of this type of crime and undertaking enforcement action wherever possible."
Louise Batchelor, spokesperson for the Partnership for Action Against Wildlife Crime Scotland, added: "We are so privileged to have freshwater pearl mussels in Scotland.
"It is just heartbreaking when criminals destroy them in reckless acts of vandalism.
"Their true value is in our best rivers not as part of the grubby, illegal trade in our precious wildlife. Everyone with an interest in the countryside can help combat this crime."
Caithness, Sutherland and Ross SNP MSP Rob Gibson welcomed action to tackle poaching.
He added: "It is sad to see piles of shells by the riverside.
"Illegal fishing of pearl mussels is a callous activity which amounts to natural vandalism."