Protesters of the controversial Plan B Trans-Canada Highway realignment project on P.E.I. say heavy rains caused silt to flow into waterways in the Bonshaw area on Tuesday.

Construction was still halted on Wednesday after rain and sediment breached retaining walls and poured mud into the river.

"We certainly had some concerns in the afternoon with the amount of rain we had," said Stephen Yeo, the chief engineer for the provincial Department of Transportation and Infrastructure Renewal.

"Some of our structure over-topped — two areas in the Bonshaw and where waste material was being stockpiled."

Transportation officials said they're now putting more mitigating measures in place, but environmentalists are concerned it may not be enough.

"There was considerable amount of rain. It overwhelmed the mitigation in place, breaching them and causing a lot of sediment to enter into the waterways," said Cindy Richards, who monitors the site for environmental opponents.

She said many of the road embankments are too steep and crews were late in hydroseeding grass.

But Yeo said hydroseeding is occurring.

"Vegetation is growing, but we're in a transition phase," he said.

"We're joining our new alignment with the old structure, there are some ditches being built and a lot of slope is being worked on which has to be seeded."

Richards said the province isn't doing enough to protect the environment during the project.

"As problems happen they try to mitigate them, but it's usually reactive measure after the fact," she said.

She said she's worried about the impact the upcoming wet months will have on the controversial project.

The realignment project, which will reroute the highway west of Charlottetown and widen the bridge in Bonshaw to three lanes, will cost an estimated $20 million, to be split evenly between the federal and provincial governments.

The provincial government contends the realignment is necessary for safety reasons. The new route will straighten the highway through Bonshaw, New Haven and Riverdale.