The Environment Agency has defended its flood response over the past two days, saying "it's difficult to stop flooding completely" when rainfall is high.
Up to 500 properties flooded in Lancashire and West Yorkshire after a month's worth of rain fell in 24 hours.
Agency spokesman Alex Ross said it had spent millions on defences that probably protected 11,000 properties.
Five flood warnings remain in place for parts of northern England, and there is one flood alert in the South West.
Flooding and heavy rain is still affecting some areas:
- In Devon, several roads are closed after stormy weather hit the county
- A Paul Weller concert in Cheshire was cancelled because of bad weather
- In Cumbria, residents are being urged to remain vigilant with the possibility of further heavy rain
- The Environment Agency said more needs to be done to improve Wales's flood defences following severe flooding earlier this month
- Nineteen canoeists were treated by paramedics - and one was taken to hospital - after getting into difficulties in a fast-flowing river in south Wales
- The promoter of the Isle of Wight Festival has apologised for the chaos caused by bad weather at the start of the event
A clean-up is under way after heavy rain on Friday and Saturday forced many people out of their homes.
Some homes in the Lancashire areas of Croston and Darwen were evacuated after nearby rivers burst their banks.
Flood warnings reduce
The Environment Agency said it had worked alongside emergency services through Friday night to clear debris, monitor river levels and operate flood defences.
But some residents have criticised the authorities' planning and response, and Labour has alleged government cuts to flood defence spending affected delivery.
Asked on the BBC News Channel about complaints the agency had been slow to respond to the crisis, Mr Ross denied that was the case.
"There were lots of flood warnings put out on Thursday and Friday through the evening across media and social media, and of course we had people out on the ground," he said.
Mr Ross said there had been "very, very high levels of rainfall falling in a very short period of time" in Lancashire and Yorkshire and that some rivers had reached their highest levels on record.
"It's important to remember that actually over the last two days round about 11,000 properties have been protected by flood defences - they're properties that would have probably flooded otherwise, based on the rain that we've seen," he said.
"We can try and predict where the rain will fall, we can try and give early alerts and warnings and we can try and build flood defences to give a reasonable level of protection but it is very difficult to stop flooding completely."
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The agency has warned people to stay away from fast-flowing, swollen rivers, and not to drive through flood water.
It has a handful of flood warnings in place in northern England and one in the South West.
The Scottish Environment Protection Agency no longer has any flood warnings in place, but flood alerts remain in three areas.
The Met Office no longer has any severe weather warnings in place.
BBC weather forecaster John Hammond said the rain was expected to ease away during Sunday, with most places settling into a "bright and breezy" afternoon.