Part of the Queensway Tunnel, linking Birkenhead and Liverpool, was closed for several hours after cracks started to appear in the concrete.
Frozen water in drains under the Liverpool-bound carriageway had expanded and caused the cracking.
Merseyrail had to carry out emergency repairs but has since re-opened the tunnel.
One lane of the Kingsway tunnel will be closed between 2100 GMT and 0630 GMT on Thursday.
There is also some disruption on the railways, with Merseyrail running a Sunday service and a reduced service operating on Northern Rail.
Some bus routes have also been affected, Merseytravel said.
The weather has also disrupted some council services - Sefton and Wirral councils have both suspended bin collections.