The flooding also caused rivers to overflow, fields to fill with water, and millions of farm animals to drown. Dozens of deaths have been attributed to the storm.
Florence made landfall as a Category 1 hurricane last week, and has killed at least 36 people, authorities said. That's twice as many people as were saved after Hurricane Matthew.
In South Carolina, emergency managers ordered about 3,000 people to flee homes along the Lynches River. Rivers at some sites are not forecast to crest for days, including near Conway, S.C.
"They got hit, but the big hit comes days later and it will be the biggest they've ever had", said Trump, who visited North and SC this week.
South Carolina Gov. Henry McMaster said the state's resources and personnel have shifted to the Pee Dee region.
"If you can get out, get out", said Joseph Tanner, the county's fire rescue chief, during an interview with WBTW News 13.
The latest death toll because of the storm is reported to be 42.
On Monday, the North Carolina Department of Transportation advised against travel in the southern, central and eastern parts of the state, noting that several sections of I-95 and I-40, which are major trucking arteries, were flooded.
In cities well inland, like Fayetteville, North Carolina, the floodwaters are continuing to rise, even as the main remnants of the storm moved over the Mid-Atlantic states and into New England on Tuesday.
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Flooding is seen in and around Wilmington, North Carolina, U.S., September 19, 2018 in this picture obtained from social media on September 21, 2018.
As environmental worries mount, Duke Energy said a dam containing a large lake at Wilmington power plant had been breached by floodwaters, and it was possible that coal ash from an adjacent dump was flowing into the Cape Fear River. "Some locations won't see rivers crest until this weekend and flooding won't subside until next week", he said in a Twitter post.
North Carolina may not be out of the woods just yet as the governor urges residents not to return to their homes. They have been serving up 20,000 meals a day to feed first responders as well as storm evacuees.
"The fire ants are doing their thing where they float and if you get close to them they will swim to you", Conway resident Debbie Long told South Carolina Public Radio.
But even as some residents remain in the grip of an ongoing disaster, officials are eyeing the road to recovery.
One road was opened into Wilmington briefly, and helicopters and military trucks were bringing relief supplies into the stranded city, where hundreds of people have been rescued from the roofs of flooded homes.
Gov. McMaster estimated damage from the flood in his state at $1.2 billion in a letter that says the flooding will be the worst disaster in the state's modern history. He stayed in state to play his college football at the University of North Carolina before being selected by the Panthers with the No. 2 overall pick in the 2002 NFL Draft.
Joe Sanderson Jr., Sanderson Farms' chairman and CEO, also said the company "will provide ice, water, food and other necessities to those affected by this catastrophic storm".
Policyholders can get up to $5,000 without an adjuster visit or providing additional documentation to their insurer, FEMA said.