Calum MacDonald, Executive Director of the Scottish Environment Protection Agency (SEPA), said investigators discovered "significant" silt pollution in rivers near the project.
The schemes contractor, Aberdeen Roads Limited, has now stopped work on the project due to risk of pollution affecting spawning ground for salon and freshwater pearl mussels.
Mr MacDonald said: "SEPA officers have been investigating multiple reports of significant silt pollution in watercourses surrounding the Aberdeen Western Periphery Route (AWPR), following heavy downpours.
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"The pollution appears to have resulted from runoff water from the construction site being flushed into smaller watercourses, including tributaries of the Rivers Dee and Don.
"Due to the potential scale of pollution, Aberdeen Roads Limited has voluntarily halted construction work on the project. This will allow for AWPR contractors to provide assurance to SEPA, within seven days, that adequate measures and monitoring are in place to protect against potential pollution.
"During this time, SEPA officers will continue to inspect the entirety of the route to identify the sources and impact of pollution on the wider water environment, which includes protected spawning grounds for Salmon and Freshwater Pearl Mussels. Transport Scotland is supporting SEPA with its ongoing investigation."
The AWPR/B-T project is one of Scotland's largest transport infrastructure schemes and is due to be completed in winter 2017.
(LM)
