Commuters faced delays as heavy rain caused disruption to the North West's road and rail network on Monday.
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, the Met Office said.
In Manchester, canal boat owners feared being swept away as water levels rose.
The Met Office said rain would return to the region on Tuesday, when a warning was in place for thunderstorms.
Roads remain closed due to flooding in Holmes Chapel, Northwich and Frodsham in Cheshire.
Part of the Manchester Airport link-road has reopened after flooding in two places, although drivers have been warned of congestion during the evening rush hour.
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 also 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.
Mavis and Jack Ripley were mopping up at their home in Turf Hill Road, Rochdale, after several properties in the town were flooded during Sunday's downpour.
The couple said a mixture of water and sewage rose through the drains into their house.
They 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 floodwater 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.
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 £290m road, which links Hazel Grove in Stockport with Manchester Airport, has been closed because of flooding since it opened in October 2018.
Cheadle MP Mary Robinson said the closure of the road was an "emergency" but there needed to be "better communication" from Stockport Council with local drivers who use the road.
'Lack of communication'
Stockport Council has apologised for its "lack of communication" with residents over the problems on Sunday and overnight.
Caroline Simpson, corporate director with the council, said: "I would like to apologise because information was absolutely key for people making journeys. If our website was not up to date I can only apologise."
A spokesman for Stockport Council said contractors responsible for maintaining the pumps were at the scene and the road would reopen when the water had "been cleared and the road cleaned".
There were no reports of airport passengers being delayed as a consequence.
The Environment Agency has lifted a flood warning covering Calderdale in West Yorkshire.
West Yorkshire Fire and Rescue Service said it had been been dealing with "widespread flooding" in towns and properties.
In the village of Mountsorrel, Leicestershire, fire crews were called to pump water from flats after a culvert overflowed.
Householders told the BBC it was the fourth time in two years they had been flooded.
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 still a flood alert in place for the Welland River which caused flooding on the A47 in Peterborough city centre on Sunday.
The Met Office 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.