The rising waters of the Pungo River caused dozens of residents to be rescued from the town of Belhaven, which had become engulfed by the raging storm.
The downtown area including the municipal building and nearby homes were swamped, starting with the high tide on Thursday evening.
Mayor Ricky Credle took refuge in the municipal building on Friday afternoon.
He said the town was “closed off” amid the highest water levels downtown he had ever witnessed.
Mr Credle said the sheriff’s department had used a high-axle truck to rescue some residents who wanted to leave, dropping them off at Red Cross shelters.
New Bern spokeswoman, Colleen Roberts, told the Associated Press more than 360 people had been rescued by mid-afternoon on Friday.
The spokeswoman revealed a further 140 were still awaiting assistance.
She said crews from the city the Federal Emergency Management Agency were working with citizen volunteers to get people to dry ground.
Ms Roberts revealed there was widespread damage and power cuts in the city but so far she had received no reports of deaths or injuries.
In total, more than three-quarters of a million power outages have been reported in the Carolinas as Tropical Storm Florence slowly makes its way across the two states, leaving destruction in its wake.
Officials at the University of North Carolina at Wilmington have expressed their annoyance that the university will remain out until further notice because of the impact of the storm.
A statement was issued to university staff on Friday which said officials “cannot yet effectively or comprehensively assess the impact on our campus”.
The university confessed it was unable to determine when it would resume the new semester.
But in its statement, the university said it would provide as much notice as possible to students and staff before it reopens.
Officials at the institution said they could not confirm how the closure will affect the rest of the academic year.