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."
People across northern Lincolnshire and East Yorkshire are cleaning up after extensive flooding along the Humber Estuary.