Debby made landfall near Bulls Bay South Carolina, about 20 miles (35 kilometres) northeast of Charleston, the NHC said in an morning advisory, warning of major floods in parts of the Carolinas and Western Virginia.
Debby made its first landfall on Florida's Gulf Coast on Monday as a Category One hurricane, packing sustained winds of 80 miles per hour.
It later weakened to a tropical storm.
Debby is now forecast to dump an additional three to nine inches of rainfall on the already soaked regions, added NHC.
"We expect this storm to continue its slow, gradual approach, bringing multiple days of heavy rainfall and the potential for widespread and severe flash flooding," said North Carolina Governor Roy Cooper in a statement on wednesday
The US National Weather Service has issued multiple tornado warnings as it forecasts that heavy rainfall will also cause "considerable" flooding across parts of the Mid-Atlantic States and Northeast until Saturday morning.
In July, at least 18 people were killed when the powerful Hurricane Beryl tore through the Caribbean before hitting the southern US states of Texas and Louisiana.
Scientists say climate change likely plays a role in the rapid intensification of storms because there is more energy in a warmer ocean for them to feed on.
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