Massive quantities of silt have been washed from excavation works and ended up deposited in fields and waterways after recent heavy rainfall. Some drinking water supplies have also been affected.
The situation, the latest in a series of similar events, has sparked fears over the impact on salmon and other protected wildlife in a special area for conservation in the Dee.
Work on the £745 million Aberdeen Western Peripheral Route (AWPR) has now been suspended to allow environmental officials to investigate the scale of water run-off and for solutions to be put in place.
But locals say the construction plan is flawed and should go back to the drawing board.
They have now written to MSPs to ask for help.
Retired scientist and Blairs resident Dr Anthony Hawkins, a salmon expert, says poor drainage measures have caused chaos and are threatening important local wildlife.
He said: “Silt can be very harmful to protected species of fish, like the Atlantic salmon, which are currently migrating upriver to their spawning grounds.
“Later in the year the silt will smother the salmon eggs that are laid within gravel in the lower reaches of the river.
“Another species that will be badly affected by silt loading is the freshwater pearl mussel, which is a filter-feeder.
“This species is severely threatened throughout Europe, and Scotland is its last remaining stronghold. The Dee has one of the healthiest populations in Scotland.
“The work being done on the road is undoubtedly causing major problems for these protected species, and perhaps for others such as otters and water voles.”
The Scottish Environment Protection Agency (Sepa)confirmed officers have been investigating “multiple reports of significant silt pollution” in rivers and burns near the new route.
John Finnie, transport spokesman for the Scottish Greens, was sent the letter.
He said: “We would hope that all relevant assessments are carried out at the earliest opportunity and address the very specific concerns legitimately raised.”
The SNP’s Maureen Watt added: “I have written to Sepa and the Scottish Government to seek assurances that work is being undertaken responsibly and without risk to our wildlife, surroundings and local homes.”
Work began on the Balmedie to Tipperty section of the bypass a year ago and is due to be completed by spring 2017.