Cooper told the president, "We're going to need your help" in the recovery efforts, to which Trump responded, "we will be there 100-percent".
It left behind deaths in at least three states and carved an arc of destruction that had not fully become clear, though one preliminary analysis said could cost up to $20 billion in property losses.
Trump, who has been criticized for his handling of Hurricane Maria in Puerto Rico previous year, also thanked first responders for their work since Florence made landfall on Friday and recapped the efforts to get food to residents and restore power.
He was accompanied by Homeland Security Secretary Kirstjen Nielsen, Federal Emergency Management Agency chief Brock Long, Senators Richard Burr and Thom Tillis of North Carolina and Senators Lindsey Graham and Tim Scott of SC.
It was the same message at Trump's first stop in North Carolina, where Gov. Roy Cooper and federal and state officials briefed the president at a Marine Corps air station in Havelock, which sits among areas Florence hit hardest. By Monday evening, 25 people were confirmed dead in North Carolina.
Patrice Carmichael, who was forced to leave her home in Lumberton at the weekend as floodwater rose, said she had been promised a hotel room for her, her partner and their four children, but they were still stuck in the Pembroke shelter as of Wednesday.
Goldsboro was also still flooded. He helped hand out hot meals and other supplies to hurricane victims, promising to do whatever is necessary to make the post-hurricane relief effort ideal. More than a foot of rain fell on the Colonial-era city and the hurricane's winds drove in water from the Atlantic Ocean, overwhelming the rivers and flooding much of the community.
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Officers were going door-to-door along the river in Brunswick County, North Carolina encouraging residents to evacuate.
The city manager told CNN that 12,000 people were "in harm's way".
A submerged auto sits surrounded by water outside a home in a flooded neighbourhood in Lumberton, North Carolina in the aftermath of Hurricane Florence.
Trump's made his whirlwind tour through the Carolinas five days after the storm, which was blamed for at least 37 deaths in North Carolina, South Carolina and Virginia.
Thousands of homes are still underwater in the Carolinas and thousands of families have had to be rescued from the floods. The area suffered significant damage, with branches down and piles of debris.
The President then met with local and state officials, SC senators Lindsey Graham and Tim Scott, and Congressman Tom Rice at the Horry County Emergency Operations Center, assuring them that Washington is behind the county and will provide federal help.
Russell Maloy walks over a railway bridge near his home to check the level of the Cape Fear River which has been rising in the aftermath of Hurricane Florence in Fayetteville, N.C. One man told the president he'd named his dog after Trump.
After submerging North Carolina with almost 1 metre of rain, the storm dumped more than 16.5 centimetres of rain in the Northeast, where it caused flash flooding.