In North Carolina, the nearly 21 inches collected in Wilmington since rain started falling Sunday topped Hurricane Floyd's five-day mark of 19 inches set in 1999, the National Weather Service said.
There were no immediate reports of injuries Thursday.
Farther north, parts of eastern Virginia were under flash flood warnings. The National Weather Service also issued a tornado watch for 33 eastern Virginia counties and 21 cities, including Richmond, Williamsburg, Arlington and the Hampton Roads area.
Flash flood watches were also in effect for areas in Maryland, West Virginia and Washington, D.C.
Much of Pennsylvania was under a flood watch. Up to 6 inches of rain were possible in Philadelphia by the time storms leave the area Friday, the weather service said.
In southeastern North Carolina, about 9 inches of rain fell at the Sunny Point military terminal in Brunswick County between midnight and 6 a.m. Thursday, the National Weather Service in Wilmington reported. Rain in the area was falling in bursts of between 1.5 inches to 3 inches per hour around daybreak, weather service meteorologist Michael Ross said.
"It's causing deteriorating road conditions," he said.
Officials urged motorists not to drive through water that was washing over roads.
"Back during Floyd, we had a lot of people lose their lives that way," Red Cross regional director Lynwood Roberson said.
The downpour came as a low pressure system from the west mixed with the remnants of Tropical Storm Nicole. Nicole dissipated over the Straits of Florida on Wednesday and its remaining rainbands were expected to remain mainly offshore while tracking northward.