Parts of the M53 and A41 were blocked due to flooding caused by heavy rain.
There were long queues on the motorway stretching back from J6 at Hooton during Monday rush hour (November 21).
A lane remains closed northbound heading towards Liverpool, but the congestion has now eased.
Highways England said there were delays of more than 30 minutes near Ellesmere Port.
The A41 was also partially blocked at Backford due to flooding with rain persistent throughout the day.
Cheshire Police advised motorists to adjust their driving to the conditions.
The latest Met Office forecast predicts the rain will continue into the early hours of Tuesday.
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