Police advised between 300 and 400 people to evacuate near the River Ouse and River Foss in York, with up to 3,500 properties at risk.
Hundreds of flood alerts and warningsare in place for England, Wales and Scotland, including more than 20 severe warnings - indicating danger to life.
PM David Cameron said the flooding was unprecedented and promised more troops.
After chairing an emergency conference call, the prime minister said the situation for many was "incredibly serious".
"The level of the rivers plus the level of rainfall has created an unprecedented effect, and so some very serious flooding," he said.
"We will do everything we can to help people in this, their hour of need," added Mr Cameron, who is expected to visit some of the flood-affected areas on Monday.
The latest flooding, which followed torrential rain over Christmas, has seen rivers burst their banks and flood waters reach towns and cities including Rochdale, Leeds and parts of Greater Manchester.
In York, officials said pumps at the Foss Barrier - where the River Foss joins the River Ouse - had been overwhelmed and flood barriers had to be lifted, meaning areas of the city that would usually be protected were now vulnerable to flooding.
York City Council said the River Ouse was expected to peak at more than 5m - close to to its highest recorded level of 5.40m.
The Environment Agency said the River Ouse's water level had reached 4.65m at 04:00 GMT on Sunday. Its typical level is between 0.5m and 1.9m.
Some of the 400 soldiers deployed across Cumbria, Yorkshire and Lancashire would be working around the Ouse which could peak at around 17:00 BST on Monday, the Department for Environment said.
A man waiting to be evacuated from his home near the River Foss in York said there were about a dozen people still in four blocks of flats surrounded by water, describing the situation as "alarming".
Police say the flood operation in Greater Manchester has now turned to "a recovery" phase, as water levels begin to drop.
More than 7,500 customers in Greater Manchester and Lancashire remain without power, Electricity North West said, including 5,500 homes and businesses in Rochdale.
In other developments:
- The Scottish Environment Protection Agency has issued a number of warnings and alerts
- "Urgent action" is required to prevent further flooding on the A55 in north Wales, Plaid Cymru say
- Red Cross volunteers are using 4x4s to transport doctors and nurses to Bangor Hospital due to flooding on the A55
- The River Aire in Leeds, where homes and roads have been flooded, reached "record levels" at 23:00 GMT on Saturday, the Environment Agency said
- Electricity North West warned power may not be restored to some 7,000 homes until Monday
- People in Rochdale, where 5,800 homes remain without power, are being urged to switch off their Christmas lights to stop further outages
- Residents of the Windsor House residential home, in York, were moved to other care homes after the basement flooded
- North Yorkshire Police said they had run out of "road closed" signs
- More than 50 people, mostly elderly residents, spent the night in a British Red Cross shelter in Bury
- Northern Rail is advising passengersnot to travel in Cumbria, East Lancashire and West Yorkshire on Sunday journey
Resident Brian Marshall said flood waters in Hebden Bridge, West Yorkshire, had been running with such force on Saturday night that sandbags had been "ripped up".
He said: "It was just impossible to do anything."
Meanwhile, Nigel Evans, the Conservative MP for Ribble Valley, called on the government to release funds immediately to help those affected.
Environment minister Liz Truss said the government will review flood defences following "unprecedented" levels of rainfall in parts of northern England.
She said it was "right to say" flood defences had been "overwhelmed".
She warned some rivers had not yet reached their expected high peak.
Kerry McCarthy, Labour's shadow environment secretary, said the government should "spare no efforts in supporting relief work" and called for better maintenance of flood defences.
On Saturday, Lancashire bore the brunt of the flooding, along with parts of Yorkshire.
People in 3,500 York properties near the River Foss, a tributary of the Ouse, were advised to move belongings upstairs and to be ready to leave.
Areas of Greater Manchester, including Salford, Bolton, Bury, Rochdale and Wigan, were also badly affected by flooding, with more than 300 flood-related calls to the fire service in 24 hours.
BBC Weather forecaster Alex Deakin said while there would be more rain in the north of England during Sunday, it would not be as intense or prolonged as the downpours on Saturday.
Meanwhile, the Met Office issued a yellow warning for ice in parts of Scotland, but no further weather warnings were in place on Sunday morning.
People can access information from council websites and the Environment Agency Floodline.
The agency is also operating a phone line - 0345 988 1188 - which will be staffed rather than offering recorded information.
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