Flooding also caused severe disruption across the road network, with the M57 closed in both directions between junction 6 at Kirkby and junction 7 at Aintree, according to National Highways.
It said the westbound M56 between junction 6 for Manchester Airport and junction 7 for Bowdon was also expected to be closed “for some time” due to flooding across all three lanes.
In Lancashire, firefighters were called to Gressingham Bridge to reports of a car stuck in the water at 21:30 on Tuesday, but the service said the vehicle was found to be empty.
The Met Office said heavy rainfall in some places could reach more than 10cm (4in) of rain.
Overnight, Greater Manchester Fire & Rescue Service said it had a high number of 999 calls due to flooding.