Up to three inches of rain was also forecast for Virginia and the Carolinas, while the northern Plains including Nebraska and Iowa were set for repeated rounds of heavier thunderstorms with wind and hail damage, and possibly even tornadoes.
"There's a storm system centered over Nashville, Tennessee, pulling moisture out of the Gulf all the way up the East Coast," Weather Channel meteorologist Kevin Roth said.
In Brookfield, Connecticut, the Still River was under a flood warning as waters reached 12.5 feet overnight, the National Weather Service said.
Portions of southern Connecticut, northeast New Jersey and southeastern New York were under flood watch, it added.
Emergency management officials in Buffalo County, Nebraska issued a flood warning for the Platte River near Kearney, which was swollen by snow melt from the Rockies. "Be prepared for rising water and ensure your neighbors are aware," it advised homeowners along the river side.
In Fayette County, West Virginia, a 17-year-old boy died and two other 17-year-old boys were injured by lightning strikes, the sheriff's office said.
There was some good news — parts of Texas and Oklahoma deluged by their wettest May on record - including deadly Memorial Day weekend floods — were finally getting dry weather. "The dry spell should allow rivers to recede a little in the southern Plains," Roth said.
However, rain is forecast for each of the next seven days — and possibly over the next 10 days — in Virginia and the Carolinas, he said.
Meanwhile, authorities in Texas late Monday formally identified two more victims of the Blanco River flood. Sue McNeil Carey, 71, and Laura Schultz McComb, 34, were identified using medical and dental records.
In total, 31 people died in floods or flood-related accidents over the Memorial Day weekend, with six people still missing.