In Windsor, about 120 miles east of Raleigh, the rising Cashie River inundated the town.
The Windsor town hall, police department, and post office were flooded and dozens of homes were surrounded by water.
Julie Hendershot, her husband, and pets were rescued Friday afternoon after the rising water had trapped them in their home.
"I woke being surrounded by water," Hendershot said.
The Bertie County, the sheriff estimated about 60 people were evacuated by rescue crews which came from as far away as Charlotte to help.
Sheriff John Holley said no one was refusing to leave, because they remember similar flooding from Hurricane Floyd.
"They're having flashbacks to Floyd, the hurricane that hit about nine years ago," Holley said.
In Pender County, the northeast Cape Fear River has risen above its banks and emergency officials say there may be 5,000 people stranded inside their homes.
Partial evacuations have been issued for Beaufort, Craven, Duplin and Pender counties to get people in low-lying areas to safety. Shelters opened overnight in Beaufort, Craven, Duplin, Hertford, Jones, Lenoir, Onslow and Pender counties.
Across the eastern part of the state, schools were canceled, roads were blocked and people warily watched rising rivers, with many expected to pass flood stage during the weekend.
State emergency planners predicted that parts of Elizabethtown, Smithfield, Goldsboro, Kinston, and Tarboro will face minor to moderate flooding into early next week.
Five deaths in North Carolina traffic accidents were blamed on the heavy rain.
Roads Closed as of Saturday include U.S 17 in several locations including south of Windsor in Bertie County, south of Maysville in Jones County and north of Jacksonville in Onslow County. Also, portions of U.S. 158 near Winton and U.S. 13 south of Ahoskie in Hertford County also closed. Several N.C. routes are closed as well, including: NC 133 near Belville, NC 50 east of Wallace, NC 561 near Harrelsville and east of Ahoskie, NC 111 southwest of Jacksonville, NC 172 near Swansboro, NC 50 near Holly Ridge and NC 32 west of Creswell
"The one good thing about this is that we had a dry September," said Charles Newman, deputy emergency management director for Pender County. "If it had been a wet month, we'd be looking at a lot more destruction."
Wilmington was soaked by its rainiest five-day period on record since 1871. The city's 22.54 inches in collected rainfall easily beat Hurricane Floyd's 19.06 inches in 1999.
Wide areas east of Interstate 95 saw rainfall of 10 inches or more, said meteorologist Scott Kennedy at the National Weather Service in Newport.
"That area saw copious amounts of rain," he said.
After about 15 inches of rain in Kinston, the Neuse River there wasn't expected to crest until Tuesday evening at three feet above flood stage, Kennedy said.
Many school districts delayed the start of classes on Friday. Localized flooding and bad road conditions led Marine commanders to close schools at Camp Lejeune and New River Air Station, and to direct military and civilian workers to delay reporting to base for two hours.
While water levels in the region's creeks and rivers rose as they did after Floyd hit in 1999, Ronald Hanchey of Wallace said at least this time he had time to prepare.
"We didn't have any warning in '99," he told The Daily News of Jacksonville. "This one right here, I'm not too afraid of it because I've got my escape route -- I've got a boat. ... We've got our deed, our insurance papers in case something does happen and food that doesn't go bad."
Near Sneads Ferry south of the Marine base, a shrimp boat took on water and sank, leaking fuel into water, the Coast Guard said.
Investigators will determine whether the boat's owner will be responsible for cleaning up the spill.
The state Department of Environment and Natural Resources warned that chemicals and untreated waste would likely pollute coastal waters. Carolina Beach and Bald Head Island were two of the coastal towns pumping floodwaters into the surf, the agency said.
"Waters impacted by this unusual storm event can contain elevated levels of bacteria that can make people sick," said J.D. Potts, manager of the Recreational Water Quality Program.
"Floodwaters and storm water runoff can contain pollutants such as waste from septic systems, sewer line breaks, wildlife, petroleum products and other chemicals."