Charleston County Sheriffs Office tweeted this photo on Wednesday evening of the flooding, and urged people not to go out into the streets
The massive storm cell killed at least two people, destroyed thousands of homes and has left 300,000 people without power.
The Battery, a sea wall and promenade district famous for its stately antebellum homes, was hammered by waves as night fell.
The water was knee-high along the streets lining the historic area - South Battery, King Street, and Murray Boulevard.
Road cones and barricades were washed away, WCBD reported. One woman was filmed leaning against the railing above the Battery, bracing as she took photos as the waves washed into her legs and boots.
The city was pumping water back into the sea, but it was not enough to stem the flow.
By 8:18pm, the tide level in Charleston Harbor was at 9.23 ft, the National Weather Service said - making it the fifth highest peak tide since records began in 1921. Warnings were in place of a storm surge of up to four feet.
The National Weather Service (NWS) Charleston warned people to avoid the beach and floodwaters.
'URGENT: Dangerous coastal inundation is going across much of the lower South Carolina coast,' they tweeted.
'Do not go to the beach and stay out of flood waters. Tide levels in the Charleston Harbor are now over 9.03 ft MLLW (3.27 ft MHHW). This is a dangerous situation!'
Mean Lower Low Water (MLLW) is the average level of the lowest tide for each day computed over a 19-year period, while MHHW (Mean Higher High Water) is the average high tide.
Smaller towns along the coast from Charleston also felt the force of Idalia which, although it was downgraded from a hurricane to a tropical storm at 5pm on Wednesday, was still generating 60mph winds, strong enough to topple power cables.
'It's a good night to stay in,' tweeted Charleston County Sheriffs Office.
'Trees are down. Roads are flooded. If you encounter street flooding, turn around. Don't drown.'
They tweeted a photo from McClellanville, 40 miles north along the coast from Charleston, of flooded streets.
On Isle of Palms, a barrier island to the north of the historic city of Charleston, police tweeted a photo of flooded streets.
'41st Avenue at Waterway Blvd has deep standing water. Avoid the area,' they said.
To the south, Folly Beach was inundated, with photos showing deep floodwater and crews trying to restore the power.
By midnight, 37,000 people in South Carolina were without power, according to PowerOutage.us, while 148,000 in Georgia and 151,000 in Florida remained cut off.
Earlier on Wednesday, a tornado ripping through South Carolina flipped a car onto its roof, leaving two people with minor injuries.
The black sedan was driving through torrential rain near Goose Creek, on the outskirts of Charleston, shortly after 2:30pm when a tornado lifted the car's two rear wheels and spun it on the hood.
The front two wheels were then lifted by the winds, and the car carried into the air - crashing down, roof to the ground, on top of another car.
Two people are known to have died in the storm so far: one Gainesville, Florida man in a car crash early Wednesday, and a second man in Valdosta, Georgia, who was killed by a falling tree on Wednesday afternoon.
The sheriff of Taylor County, Florida - where landfall was made at 7:45am on Wednesday - said on Wednesday evening that so far there have been no reports of deaths or serious injuries, despite the 125mph winds.
Reader Comments
.
"Did Hurricane Idalia follow a trajectory that was laid out by nature? Or is there much more to the equation of Idalia's path? The US military first initiated hurricane modification operations in 1947 with project Cirrus, how far have they advanced their technology in the last 76 years? What part do frequency transmission installations play in the steering of Hurricane Idalia and every other hurricane that the controllers use to carry out possible agendas and objectives?..."