Floyd produced 24 inches of rain in some parts of the state, while Florence has already dumped about 30 inches in areas around Swansboro.
Authorities ordered the immediate evacuation of up to 7,500 people living within a mile (1.6 kilometers) of a stretch of the Cape Fear River and the Little River, about 100 miles (160 kilometers) from the North Carolina coast. "We also surmised the storm was not going to be near as severe as it was".
But with radar showing parts of the storm over six Southeastern states and flood worries spreading into southern Virginia and West Virginia, North and SC were still in the bull's-eye.
Florence, which made landfall in North Carolina as a Category 1 hurricane on Friday, has left at least eight people dead.
Scores of shelters were open Sunday, filled with people who fled ahead of the storm and some of the hundreds more who have been evacuated from their homes by rescue workers in boats and helicopters.
Weakened to a tropical depression early Sunday after blowing ashore as a hurricane with 90 miles per hour (145 kph) winds on Friday, Florence was still spinning slowly atop the Carolinas as it pulled warm water from the ocean and hurled it onshore.
Earlier Sunday, officials from the Cape Fear Public Utility Authority had said they were nearly out of fuel for the water plant and might have to shut down.
Jon Schuppe reported from Wilmington, North Carolina.
Some rivers were not expected to crest until Monday or Tuesday, the National Weather Service said.
Trogdon said the state was working with the Department of Defense and National Guard to see if they could get first responders through to Wilmington in high-water vehicles. Farther along the Cape Fear River, grass and trees lining the banks were partly submerged.
Florence has weakened into a tropical depression but flash flooding and major river flooding are expected to continue over significant portions of the Carolinas.
More than 641,000 homes and businesses were without electricity in North and SC and surrounding states, down from a peak of almost 1 million. "We feel fully supported". More than 360 people have been carried to safety since Thursday night amid rising waters from a river swelled by both rain and salty storm surge.More news: Warframe on Switch launches this November
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Gov. Henry McMaster issued an executive order lifting evacuation orders for Charleston, Berkeley, Dorchester and the Edisto Beach area of Colleton County effective at noon Saturday.
The National Weather Service continues to warn of life-threatening flash flooding and river flooding.
A campaign sign is under water on Pamlico St in Belhaven, N.C. on Saturday morning on September 15, 2018. Even by week's end the city could be experiencing minor flooding from the river.
Meanwhile, central and western North Carolina, far northern SC and southwest Virginia were expected to get an additional 5 to 10 inches of rain, with total accumulations of 15 to 20 inches likely, elevating the risk of landslides, the center said. Radar is estimating that some areas between Wilmington and New Bern, North Carolina, have received over 30 inches of rain. He told ABC's "This Week" on Sunday that Florence's combination of heavy rainfall, extreme storm surge and high winds makes the storm "one for the record books". The IRS took similar measures for those affected by Hurricanes Irma and Harvey previous year. Just last month, Lane dropped a maximum of 52.02 inches of rain in Hawaii, breaking the state record.
The mayor of New Bern, North Carolina, says his city has imposed a curfew.
Florence also now stands as the sixth-highest tropical cyclone rainfall total across the US for records dating back to 1950.
The major highways into the area, Interstate 40 and USA 74, were not accessible, officials said.
The rain was unrelenting in Cheraw, a town of about 6,000 people in northeastern SC.
North Carolina is bracing for what could be the next stage of the still-unfolding disaster: widespread, catastrophic river flooding from Florence.
Florence is still moving very slowly inland. Florence will likely become a remnant low within 36 hours. Daniella Silva reported from NY.
"People need to heed the warnings from their local emergency management experts and stay in safe ground", the Coast Guard's Adm. Schultz said.