The rain is focused on the Carolinas through Thursday and then will move north.
Tropical Storm Debby is slamming the Southeast with heavy rain after making landfall in Florida as a Category 1 hurricane on Monday.
At least six people have been killed in Florida and Georgia.
The highest rain total so far is south of Tampa, Florida, where about 19 inches of rain fell.
In Georgia, more than 11 inches of rain struck northwest of Savannah, and in South Carolina, 14 inches of rain was recorded between Charleston and Hilton Head Island.
On Tuesday afternoon, Debby is located about 10 miles southeast of Savannah and is crawling north at a very slow speed.
The heavy rain will stretch from Charleston to Wilmington, North Carolina, on Tuesday. Storm surge could reach 4 feet from Savannah to Cape Fear, North Carolina, and tornadoes are possible.
Flash flood warnings are in effect for Savannah, Charleston and Myrtle Beach, South Carolina. Rainfall rates could reach 1 to 2 inches per hour during the heaviest downpours, which will bring more flooding.
The worst of the rain is expected along the South Carolina-North Carolina border through Thursday evening. A rare "high risk" for flash flooding was issued from Charleston to Raleigh, North Carolina, where rain totals could climb to 25 inches through Thursday.
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More than 1,100 flights have been canceled within, into or out of the U.S. on Tuesday as Debby slams the Southeast and thunderstorms strike the Northeast. Ground stops are in place at the New York City area's three airports.
The threat of severe flooding is very high across South Carolina with Tropical Storm Debby "creeping across our state," South Carolina Gov. Henry McMaster warned on Tuesday.
The rain from the slow-moving storm may be particularly heavy from Myrtle Beach to the North Carolina border, the governor said.
Forty-eight state roads are closed due to flooding and 50 high-water vehicles are at the ready to respond, he said.
More than 90,000 customers remain without power in Florida, more than 24 hours after Debby tore through the state.
"Restoration is taking longer in areas with flooding and heavy vegetation, as crews must wait for the water to recede and clear through debris before they can restore power," Florida Power & Light said Tuesday morning. "Rest assured, we’ll continue working until everyone who can safely receive power is restored. Avoid these flooded areas and stay away from downed power lines."
A curfew in Charleston, South Carolina, has been extended to 7 a.m. Wednesday as the flood-prone city braces for potentially life-threatening flooding.
"Residents are advised to stay off the roads unless there is an urgent emergency," the Charleston Fire Department said.
Charleston is under a flash flood warning. Up to 1 foot of rain has already fallen in the city, with more to come.
