Professor Anthony Hawkins, former head of the Marine Laboratory in Aberdeen, said silt could cause major damage to the mussels in the River Dee.
The river is one of the few places where they are still found, having died out across many parts of Europe. But it is feared the construction work on the £745 million bypass around Aberdeen could impact on the species and other wildlife in the area.
Last month work was stopped temporarily to allow the Scottish Environment Protection Agency (Sepa) to investigate alleged damage being done to the river.
Contractors have now returned to parts of the site of the Aberdeen Western Peripheral Route (AWPR) in a “phased” approach as Sepa continues to make inquiries.
Heavy downpours in the North-east led to silt pouring into the tributaries of both the region’s majors rivers – the Dee and the Don – with contractors halting work while solutions were sought.
A group of five Deeside residents wrote to their MSPs raising concerns over wildlife caught up in the alleged fallout from the construction work.
And Prof Hawkins fears that the road construction may have a long-term impact on flora and fauna.
He said: “There were reports of water being emptied into woods and fields filled with silt causing damage to species there.
“I shudder to think what this could be doing to freshwater pearl mussels in the Dee.
“They have mostly died out throughout Europe over the past 50 ears and the Dee is one of the few places left where they are found.”
Meanwhile, Calum MacDonald, executive director of Sepa, has vowed that the agency will continue working with contractors to ensure strict protocols are kept in place.
A Transport Scotland spokeswoman said: “We take our environmental responsibilities seriously and will also continue to work with the contractor to ensure that watercourses are protected.”
The long-awaited bypass will connect one of Scotland busiest roads, the A90 at Stonehaven on the south side of Aberdeen, with the Blackdog area to the north.