In Sheffield emergency services have been striving to rescue dozens of people stranded in the Brightside area.
A 28-year-old man died in Hull after becoming stuck in a drain despite the attempts of rescuers to free him.
Also in Sheffield, a body has been found after a 13-year-old boy was swept away in a river, and a 68-year-old man died getting out of his car in floods.
Weather systems
Forecasters said June's average rainfall of about 50mm could fall during a period of 24 hours, with up to 75mm in some places, and severe flood warnings are in force in many areas.
An area stretching from north-east Wales through the north Midlands, Lincolnshire and Yorkshire was expected to see more than 25mm of rain.
Phil Rothwell, head of flood defence at the Environment Agency, said "unprecedented weather systems" were causing "very difficult circumstances".
South Yorkshire Police said they discovered a body in a swollen river in Millhouses Park in Sheffield, a quarter of a mile downstream from where a search was being carried out for the 13-year-old.
The 68-year-old died when he was swept away by floodwater after getting out of his car in the Wicker area of Sheffield.
Two four-man specialist river rescue crews and their boats from Hereford and Worcester fire service have been sent to Sheffield to help the South Yorkshire brigade.
"There are quite a lot of people on rooftops that look quite desperate and the rescue services are trying their best to take them off"
Three people were rescued by helicopter from a Sheffield building after they were stranded on the second floor of a Forgemasters factory in Brightside Lane.
Dozens of other people have also been stranded in the same area, rescue services said.
The man who died in Hull had become trapped in neck-deep water when he went to help his grandfather clear a flooded drain in the Hessle area.
Glenn Ramsden, from Humberside Fire and Rescue Service, said: "It's been an absolutely desperate operation to save this man, but at the end of the day we couldn't do it."
Rising waters
In Leeds roads became flooded making even short journeys impossible, livestock came under threat as fields flooded in Gloucestershire, and north Wales was also affected.
People were rescued by helicopter in Brightside, Sheffield The weather: Your pictures
At Corwen, Denbighshire, the A5 was reported to be knee-deep in water and many cars forced to turn back, and parts of the town centre were flooded.
Waters are continuing to rise overnight on the river at Tenbury Wells in Worcestershire.
In Lincolnshire, a nine-year-old boy was earlier rescued by passers-by from the swollen River Lud in Louth.
And in Derbyshire, a rescue helicopter and fire crews were travelling to Staveley after reports of a man stuck up a tree.
On the railways, Central Trains, Chiltern Railways, First Capital Connect, First Great Western, Transpennine Express and Virgin Trains have all warned of disruption to services due to the weather.
Animals rescued
About 100 people in Lowdham, Nottinghamshire, 60 homes and businesses in Louth, Lincolnshire, 200 residents of Winn Gardens, Sheffield, and 70 houses in the Halton area of Leeds were evacuated, with occupants moving to emergency centres.
KEY ROAD PROBLEMS
In Cheltenham, Gloucestershire, the fire service was inundated with reports of flood water entering cellars in shops and homes, and in nearby Gloucester fire crews rescued 50 dogs and 20 cats stranded in kennels.
Further south in Bideford, north Devon, heavy rain caused streams to overflow their banks, flooding properties.
The Environment Agency has issued 22 severe flood warnings and 129 standard flood warnings.
Severe warnings are in place in north-east England, the Midlands and over much of the east of the country.
When taking photos or filming please do not endanger yourself or others, take unnecessary risks or infringe any laws.
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