Later in the day, trees could be seen on top of roofs, driveways and parked cars.
Isaac, which had built to tropical storm status when its winds topped 39 mph on Saturday, has weakened to a depression over the eastern Caribbean sea with winds of 35 mph and is moving west at 15 mph, lashing the Lesser Antilles with rain squalls as of the 5 a.m. advisory.
Elsewhere in the storm-ravaged state a man died plugging in a power cord, and a woman died from a heart attack after rescuers were unable to reach her home past downed trees.
The city said two FEMA teams were working on swift-water rescues and more were on the way.
Residents at Trent Court Apartments wait out the weather as rising water gets closer to their doors in New Bern, North Carolina.
Tropical storm-force winds extend outward up to 175 miles (280 kilometers) from its center.
Just a few minutes before the now-Category 1 storm made landfall, cameras on board the International Space Station managed to catch the mesmerising footage below. Authorities have advised people, however, to move to higher levels in their homes while they wait to be rescued. Others could only wait and hope someone would come for them.
Forecasters warned that drenching rains of anywhere from 1 to 3½ feet as the storm crawls westward across North and SC could trigger epic flooding well inland over the next few days. The coming storm surges and heavy rains will cause severe flooding that may submerge parts of the Carolinas in up to 40 inches of rain.
"I had a lot of fear initially but I'm glad to be inside and safe", said Zelda Allen, 74, a retired tax accountant from Hampstead, North Carolina, who was riding out the storm at Wilmington's Hotel Ballast with her husband. "The storm is wreaking havoc on our state".
About150 people were awaiting rescue in New Bern, N.C. early Friday morning, and multiple news outlets report some 60 people had to be evacuated from a motel in Jacksonville, N.C. overnight after it sustained structural damage as the Category 1 hurricane made landfall. Significant weakening is expected over the weekend.
"This is unsafe, risky times in New Bern".
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. According to Fire Chief Glen Rogers, there are in fact only 12 people left on the beach to sit out the storm.