Many train services were disrupted across the UK, with buses having to replace trains on some routes in the North East.
Numerous roads were still impassable, with Worcestershire, County Durham, Tyne & Wear and Northumberland among the most badly-affected areas.
Many roads in Yorkshire also had to be closed due to the floods. These included roads in Scarborough, Catterick, Stainton and Conisbrough.
Flooding also caused disruption to train services at Darlington in north east England, with Durham, York, Darlington and Doncaster among stations affected.
Passengers trying to use the East Coast Main Line were urged not to travel if their journey involved the York to Newcastle section. “Overhead wire problems” at Darlington were to blame, according to the East Coast website.
An East Coast train company spokesman said: “We are advising passengers not to travel today between York and Newcastle due to problems with the track and infrastructure caused by flooding.
“The East Coast route is currently blocked in the Aycliffe area, north of Darlington, due to damage to the infrastructure. In addition there is continued flooding at Eryholme, south of Darlington.
“Services between York and Newcastle are expected to be disrupted throughout the rest of today and our advice to passengers whose journey involves travel between these destinations is not to travel today unless your journey is essential.”
He went on: “We would like to apologise to passengers for the disruption caused to services today.”
Parts of Yorkshire have been among the worst affected areas with a hospital forced to cancel all its operations yesterday because of rising floodwaters.
The Environment Agency has issued 24 flood warnings across Yorkshire and the North East and forecasters were warning that the heaviest rain was still to come.
Firefighters pumped water from the grounds of the Friarage Hospital, in Northallerton, yesterday after a nearby stream overflowed.
An NHS spokesman said three theatres had been closed due to drainage issues, resulting in ten operations being cancelled.
She added: “As a result the trust has made the decision at 11.30am to cancel all elective (planned) surgery today. The occupational therapy department has also had to close.
“Along with the fire service, the staff are working hard to keep the hospital working as normal and we are continuing to monitor the situation.”
Elsewhere a pensioner was rescued from his car after becoming trapped in flood waters under a railway bridge.
Northamptonshire Police said officers found the car and rescued the man, who received medical treatment and was later arrested on suspicion of drink-driving.
Flooding led to road closures including the A1(M) northbound near Catterick Garrison and the A19 near Northallerton as well as train delays and cancellations around the region.
Wetherby Racecourse has postponed a meeting due to be held tomorrow after the rain left the track heavily flooded.
Firefighters from North Yorkshire were called to a number of incidents, including removing vehicles from flood water and pumping out water in the Northallerton area and dealing with flooding at homes in Stokesley, Thirsk and Knaresborough.
Council bosses in the region were also investigating whether the strong winds and heavy rain had caused a school roof to collapse over the weekend.
Hull Council said the damage at St Thomas More Roman Catholic Primary School may have been caused by the weather.
Forecasters have predicted heavy deluges over the next 24 hours with up to 30mm expected with North Yorkshire one of the worst affected areas in the country.
Weather radar images last night showed Scarborough faced up to 5mm of rain an hour as storms swept in off the North Sea.
As heavy rain and wind left a trail of destruction across Britain, Government and insurers clashed about how future flooding bills would be covered.
Environment Secretary Owen Paterson attacked the insurance industry for causing flood victims “alarm” after 200,000 householders were warned they could lose their home cover.
Insurers have called on the Government to provide a temporary overdraft facility to pay claims for high-risk households in the event of serious flooding such as that seen in 2007.
Nick Starling, director of general insurance at the Association of British Insurers (ABI), accused ministers of rejecting its proposals.
“We want a solution even more now after the difficult events of the weekend,” he said.
However Mr Paterson criticised the ABI for airing its concerns at the height of the crisis.
“I think it is actually rather demeaning at this particular moment in time to be talking about this. It is rather a shame that it has been raised at this particular moment when there are a lot of distressed people with flooded homes,” he said.