More than 130 flood warnings are still in place for England and Wales, including 22 in Sussex, Kent and Hampshire.
Thousands of home-owners in flood-prone areas have been warned by the Environment Agency (EA) that flooding of some homes may be "virtually inevitable".
Around 100 houses in Chertsey, Surrey, flooded on Thursday evening after the River Bourne broke its banks.
At least 50 people have been evacuated from their homes in the area.
A man from north London also died on Thursday after attempting to clear a blocked drain.
Alan Higgs, 58, from Chingford, was helping a neighbour affected by high levels of flood water.
Heavy rain
A 45-year-old angler died after "horrendous" rain and force six gales swept him off Amble pier in Northumberland.
An inshore lifeboat capsized during a rescue attempt and three crew members required hospital treatment.
The flooding has caused disruption on the roads and the railways for many commuters returning to work on Thursday after the Christmas and New Year break.
The EA warned of the serious risk of flooding after weather forecasters predicted a further inch of rainfall for the South East, South Wales, East Anglia and the Midlands before nightfall.
"
The rivers are right up to the tops of the banks and they just cannot take any more
"
Ray Kemp, Environment Agency
EA spokesman Ray Kemp said: "The rivers are right up to the tops of the banks and they just cannot take any more.
"This amount of rain coming through cannot get into the rivers and the only place it can go is into people's homes."
Mr Kemp warned motorists to be "very wary" of widespread road flooding, which could be so severe cars would be in danger of being swept away.
In Hertfordshire the northbound M1 was closed between junctions 1 and 5 during the morning rush hour after a fatal accident.
TALKING POINT
Flooding: Have you been affected?
"
His garden is so sodden he is thinking of growing rice or trout!
"
Rob Glehdill, England
Rail commuters faced disruption on some services following the derailment of a train from Brighton to London near Redhill, Surrey, after it hit a landslide on New Year's Day.
Network Rail services between London and the south coast are affected by the incident.
Trains on South Central, Thameslink and the Gatwick Express are expected to run on reduced timetables.
Journeys from London and South Wales will take up to an extra hour because of flooding in tunnels while journeys between London and the South West will take an extra half hour.
People in flood-prone areas have been urged to protect their homes and property.
The EA's head of flood defence David Rooke said "remarkably few" properties had flooded so far, but he was expecting more to do so over the next two days.
But he said the situation had improved since flooding brought chaos to parts of the country in October 2000.
"Overall we have improved some 70km of defences and have protected about 25,000 people since two years ago," he told BBC Radio Five Live.
The EA's flood information website has repeatedly crashed under the sheer weight of traffic using the site.
For the latest information, the Environment Agency advises people to call Floodline on 0845 988 1188.