The Met Office had issued an amber warning for rain across swathes of Lancashire and Greater Manchester until 09:00 GMT, while a yellow warning also covers parts of Merseyside and Cheshire until 11:00.
Dozens of flood alerts are also in place.
Flooding on the line between Manchester Piccadilly and Manchester Airport train stations has also led to major disruption and cancellations.
In Warrington, three people were rescued from a car by Cheshire Fire and Rescue Service on Cliff Lane, and in Booth Lane, Lymm, another three people were rescued in the early hours.
The service used a rescue raft to get to the vehicles in both cases.
