A combination of high tides and strong winds caused a storm surge which overtopped flood defences.
Hundreds of properties were evacuated with residents moved to emergency shelters.
The Environment Agency said the tide on Thursday that caused the damage had been the highest since 1953.
More than 500 properties were evacuated in the village of Keadby, near Scunthorpe, after a hole opened up in the bank of the River Trent.
The Environment Agency said about 50 buildings in the village flooded after high tides. Others were evacuated in nearby Burringham on Thursday.
One Burringham resident said the village's main street was "like a river" when the water flooded over the riverbank.
"It's a bit devastating really, the damage it's caused," he said.
"I haven't seen anything like that before.
"The banks were like paper, just floating away when it went."
Up to 100 properties have been flooded in Reedness in the East Riding, with some residents taken to Goole leisure centre.
Homes in Gunness, Amcotts and South Ferriby in North Lincolnshire have also been evacuated.
In Hull, residents living on some streets in the city centre were also removed to safety.
Some hotels and shops near the city's waterfront lost power and were flooded.
Philip Woods, manager of the Ibis Hotel in Hull, said all of the ground floor area was under water.
"The surge of the water came into the hotel came down the long corridor and came into the rooms," he said
Road and rail links to Hull were also affected.
Part of the A63 in the west of the city was closed on Friday morning after water from the Humber covered the carriageway.
Rail services in Hull and parts of North Lincolnshire were suspended.
Richard Hannigan, chief fire officer at Humberside Fire and Rescue Service, said firefighters had saved 181 people from flood water.
"We've moved now from the rescue phase into the recovery phase," he said.
"We're putting out our high-volume pumps to start pumping out the residual water that of course is trapped in by the sea defences."
Firefighters have been pumping water away from Hessle foreshore next to the Humber Bridge.
James Jackson who lives next to the bridge said he thought it would be at least six months until his flooded home was back to normal
"There'll be no Christmas party or anything this year," he said.
"It's just going to be trying to get a resemblance of life again."

In the past five years, 17,982 complaints have been lodged with the county's borough and district councils.
Of those, 3,454 relate to dogs barking, the BBC Radio Suffolk Freedom of Information request found.
Seven thousand complaints were made about loud music and parties, while church bells have led to 10 complaints to councils.
Other complaints were made about bird scarers in fields, machinery and vehicle noise, and people shouting or talking loudly.
17,982
Total number of complaints
3,454 about barking dogs
336 about bird scarers
16 about fireworks
10 about church bells
Ipswich Borough Council received the highest number of complaints over the five years, with 4,568.
Waveney District Council received 3,672 complaints, while Suffolk Coastal District Council had a total of just over 3,000.
Mark Johnson, senior public health officer at St Edmundsbury Borough Council, said the best thing for people to do was to speak with the person making the noise.
"It's the most common sense approach because sometimes they don't even realise they're causing a nuisance to their neighbours," he said.
As for dogs, Candice Rose, owner of Canine Creche in Martlesham, said they could be taught not to bark.
"The key thing is reward and distraction," she said. "We distract them and then reward the good behaviour.
"There are solutions, it could be a behavioural issue, in which case that can be adjusted, but if it's just through boredom - there really is no excuse in this day and age."
People across northern Lincolnshire and East Yorkshire are cleaning up after extensive flooding along the Humber Estuary.
[NEXT_CONCEPT]
Barking dogs account for about a fifth of all noise complaints in Suffolk, it has emerged.