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.
Greater Manchester Fire and Rescue Service has asked that members of the public only call 999 in emergencies and said concerns about flooding should be reported to local authority hotlines.
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.
In Preston, Lancashire, fire crews were called to rescue two people and a dog from the River Ribble at 16:00 BST on Sunday.
BBC Radio Manchester reporter Anna Jameson reported that a pump to help keep the A555 clear of water had failed.
It is the second time the road, which links Hazel Grove in Stockport with Manchester Airport, has been closed because of flooding since it opened in October 2018.
The Environment Agency has removed a flood warning for Peterborough, but said it was still monitoring river levels, although it did not expect them to rise.
There is a still a flood alert in place for the Welland River which caused flooding on the A47 in Peterborough city centre on Sunday.
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.
She said there would be fine weather for much of England and Wales on Monday before low pressure brought heavy showers into the South West overnight.
A weather warning for “frequent and widespread” thunderstorms was in place for Tuesday as the rain moved to northern and eastern parts of the UK.
There are currently 15 flood warnings issued by the Environment Agency covering Calderdale, West Yorkshire.
The warnings include the river Calder at Todmorden and Hebden Bridge, which was badly hit by the 2015 floods.
West Yorkshire Fire and Rescue Service said it had been been dealing with “widespread flooding” in towns and properties after prolonged heavy rain hit the area.