WSDOT said the closures can be expected today through a week from today.
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Drivers are encouraged to use an alternate route around the work area to avoid the expected delays.
As of 1:55pm, southbound traffic was backed up about 2.5 miles to the Meridian Street interchange.
"Our priority is keeping the roadway safe for all users and we need to shift our resources moving into the winter months."
As of 3:25pm, all lanes were reported to have been reopened.
No one was injured but northbound I-5 is expected to be reduced to 1 lane through the evening commute.
A lead pilot car warned the semi truck driver not to attempt to go under the overpass so they could stop before striking it.
9:45am - Ferry officials say the Whatcom Chief has been returned to service.
Road striping will be done across 11.5 miles of road.