At least four people were killed.
Forecasters said Florence's surge could cover all but a sliver of the Carolina coast under as much as 3.4 metres of ocean water, and days of downpours could unload more than 0.9 metres of rain, touching off severe flooding.
Elsewhere hundreds more had to be rescued from rising waters, with some residents having to climb up to their roofs to escape danger.
Forecasters said that given the storm's size and sluggish track, it could cause epic damage akin to what the Houston area saw during Hurricane Harvey just over a year ago, with floodwaters swamping homes and businesses and washing over industrial waste sites and hog-manure ponds.
Governor Cooper said the hurricane was likely to "continue its violent grind across the state for days". He said parts of North Carolina had seen storm surges - the bulge of seawater pushed ashore by the hurricane - as high as 3.5m.
A mother and her infant were killed in Wilmington when a tree fell on their home on Friday.
A woman died from cardiac arrest in the town of Hampstead after emergency responders had their route to her blocked by downed trees, a county official said.
Florence made landfall as a Category 1 hurricane at 7:15 a.m.at Wrightsville Beach, a few miles east of Wilmington and not far from the SC line, coming ashore along a mostly boarded-up, emptied-out stretch of coastline.
Once a Category-4 hurricane with winds of 225kph, the hurricane was downgraded to Category 1 on Thursday night. "I'm not sure if it's a shift in the wind or low tide - but the water has miraculously disappeared".
Many US residents seek shelter from hurricane at Myrtle Beach resort
Massive evacuations were ordered along the state's barrier islands and in cities and towns along the direct path as a result. Among those feeling the impact of the stormwere local farmers, whose tobacco and corn harvests had not been completed.
This landfall has been a long time coming: The hurricane arrived more than two weeks after the National Hurricane Center issued its first advisory for the storm. Other communities got well over a foot.
Five to 10 inches of rainfall will produce life-threatening flash flooding in North Carolina, South Carolina, and southwest Virginia.
Preparing for the worst, about 9,700 National Guard troops and civilians were deployed with high-water vehicles, helicopters and boats that could be used to pluck people from the floodwaters.
The National Hurricane Center said Florence will eventually break up over the southern Appalachians and make a right hook to the northeast, its rainy remnants moving into the mid-Atlantic states and New England by the middle of next week.
Hurricane Florence is "wreaking havoc" along the U.S. coast and could wipe out entire communities, North Carolina's governor has warned. That's enough to fill the Chesapeake Bay or cover the entire state of Texas with almost 4 inches of water, he calculated.
Cline said July was the wettest ever in that part of North Carolina, and the water table rose 21 inches higher than normal.
"The worst of the storm is not yet here, but these are the early warnings of the days to come", North Carolina Governor Roy Cooper told reporters just before the hurricane made landfall. The streets were mostly deserted and some were blocked by fallen trees.
A wind gust at the Wilmington airport was clocked at 105 miles per hour (169 kph), the highest since Hurricane Helene in 1958.
Airlines canceled more than 2,100 flights through Sunday.
"WE ARE COMING TO GET YOU", the city of New Bern tweeted earlier Friday. "You may need to move up to the second story, or to your attic, but WE ARE COMING TO GET YOU", the authorities in New Bern said on Twitter. He says that "over the years the state government and the federal government have become very coordinated in their ability to manage the pre-deployment of assets (and) the response to the citizens of those states, and we will soon be into the recovery".