Rush hour commuters faced delays as heavy rain continued to cause disruption to the North West’s road and rail network.
Trains were cancelled between Manchester and towns including Wigan and Stalybridge. The A555 Manchester Airport Relief Road remained closed.
The equivalent of half a month’s rain fell on the region in the space of 24 hours, said the Met Office.
In Manchester, canal boat owners feared being swept away as water levels rose.
The Environment Agency had 12 flood warnings in place across the North West on Monday morning and said water levels would continue to rise.
There were also flood warnings in Yorkshire and the Midlands.
National Rail said trains were unable to run between Manchester Victoria and Todmorden in West Yorkshire because of flooding, while the A34 in Alderley Edge, Cheshire was closed.
Met Office meteorologist Helen Roberts said 100mm (4in) of rain – more than the 89.5mm monthly average for July – had fallen in Rochdale in 48 hours over the weekend.
Several properties were flooded in Rochdale, including the home of Mavis and Jack Ripley in Turf Hill Road.
The couple said a mixture of water and sewage rose through the drains into their house and have called for the local authority to improve drainage after a number of similar floods in recent years.
Rochdale Council has been approached for comment.
Greater Manchester Fire and Rescue Service said it had dealt with 116 emergency calls in 24 hours up to 08:00 BST on Monday.
The brigade dealt with flooding in Sale and Rochdale and used a boat to rescue five people trapped in vehicles surrounded by flood water in Stannybrook Road, Failsworth, at 19:50 on Sunday.
Photographer Ashley Stocks spoke to owners of canal boats moored at Castlefield in Manchester on Sunday night who feared fast-flowing water could wash their barges away.