The National Hurricane Center said the storm would dump as much as 30 to 40 inches (76-102 cm) of rain on the southeastern coast of North Carolina and part of northeastern SC, as well as up to 10 inches (25 cm) in southwestern Virginia.
North Carolina activated 2,800 National Guard personnel, and SC called up 2,100 of its National Guard soldiers to be ready to aid in recovery efforts once the storm has passed. "Catastrophic effects will be felt".
A buoy off the North Carolina coast recorded waves almost 30 feet (9 meters) high as Florence churned toward shore.
Warning of looming storm surges of nine to 12 feet (2.7-3.6 meters), he urged residents to take the storm seriously no matter the category, saying "this is all about the water anyway".
Florence's winds weakened as it drew closer to land, dropping from a peak of 140 miles per hour (225 kph) earlier in the week, and the hurricane was downgraded from a terrifying Category 4 to a 1. The actual landfall - when the center of the eye reaches land - will be Friday afternoon at the earliest, said Neil Jacobs of the National Oceanic and Atmospheric Administration.
And in Wilmington, North Carolina, a steady rain began to fall as gusts of winds intensified, causing trees to sway and stoplights to flicker.
The shelter had been set up in a school and was offering temporary refugee from the elements to around 400 people on Thursday, although it had a capacity for up to 1,200 in the popular seaside resort.
"We live in a mobile home so we were just like 'No way, '" she said. "Because I don't know that we can go in and get you". "But can't replace us, so we made a decision to come here", said the 39-year-old.
Officials warn of life-threatening storm surges in both North and SC as the hurricane moves towards land with maximum sustained wind speeds of 90mph (150 km/h).
Forecasters said conditions will only get more lethal as the storm smashes ashore early Friday near the North Carolina-South Carolina line and crawls slowly inland.
Florence had been a Category 3 hurricane with 120 miles per hour winds on Thursday but dropped to Category 1 before coming ashore.
Forecasters continue to warn of storm surges, excessive rainfall and catastrophic flash flooding.
A tornado watch was also in effect for parts of North Carolina.
This vulnerable area has been under mandatory-evacuation orders since Wednesday night at 8 p.m., and those who are choosing to ride out the storm have been under a mandatory curfew since that time, to keep people inside.
FEMA's Long warned the danger was not only along the coast: "Inland flooding kills a lot of people, unfortunately, and that's what we're about to see", he said.
About 10 million people could be affected by the storm and more than 1 million were ordered to evacuate the coasts of the Carolinas and Virginia.
One resident from Myrtle Beach, a popular SC destination for tourists, told CNN: "We're well prepared".
As the storm approached, Michael Cramer, the town manager of Carolina Beach, N.C., told NPR's Morning Edition that "easily a third of our community will be underwater" if the worst predictions are fulfilled.
Officials in several states have declared states of emergency, including in the Carolinas, Georgia, Virginia and Maryland, where coastal areas are still recovering from summer storms.
Duke Energy Corp, the biggest utility in the area with over 4 million customers in the Carolinas, estimated the storm could cause between 1 million to 3 million outages.
Cooper said Florence was set to cover nearly all of North Carolina in several feet of water. An investigation is underway, but officials said it appears there's no reason for others at the shelter to worry.