Fourteen inches of rain deluged Clarksdale, Mississippi, and 12 inches fell in Greenville, authorities said. The towns sit on or near the Mississippi River.
Another 100 homes flooded in the Pine Belt region of the state after Meridian received up to a foot of rain, authorities said.
Add flooding along the Gulf Coast, and the disaster became a triple assault. In all, 400 homes flooded in Mississippi.
"This is a pretty historic event. We've had a threefold event in ... 48 hours. Looking for another 48 hours of impacts due to rains," Mississippi Emergency Management Agency Director Lee Smithson said.
Meanwhile, storms and flooding prompted calls for residents to move to higher ground in Louisiana and forced the shutdown of some New Orleans schools.
Fears of levee breaches grew.
"Seek higher ground now!" the National Weather Service said, warning of a flash flood emergency Friday for Louisiana's Tangipahoa Parish and the city of Hammond.
Gov. John Bel Edwards declared a state of emergency, and the weather service issued a flash flood emergency for several other parishes
Mississippi Gov. Phil Bryant also declared a state of emergency, and officials warned of flash flooding
"The water's still rising," said David Burford, the Washington County, Mississippi, emergency management director.
One dead in Texas, 3 in Louisiana
Storms across the region have left at least four people dead, officials said.
In Texas, a man died after his kayak capsized in Dickinson Bayou near Galveston, police said.
Three people were killed in Louisiana, the governor said. In one case, a driver died when floodwaters swept his vehicle off a road in Bienville Parish, a spokesman for the Governor's Office of Homeland Security and Emergency Preparedness said.
New Orleans shut down some schools Friday because of flash floods. Officials warned that floodwaters could rise above a levee and jeopardize thousands of homes.
In Tennessee, Shelby County Sheriff's Office deputies went door-to-door Friday using an amphibious vehicle to save people trapped by rising water near the Loosahatchie River, including an 87-year-old man with a medical condition, CNN affiliate WMC-TV reported.
Flood risks until Monday
The region is at risk of further flooding until Monday.
State government offices in 40 parishes were to be closed
through Friday, according to Commissioner of Administration Jay Dardenne. The northwest part of the state could see another 8 to 10 inches on top of the drenching
of more than 14 inches already in some areas.
In Bossier Parish, officials said they had closed at least 100 roads.
They issued a mandatory evacuation order this week for residents of 3,500 homes that could be at risk if floodwaters keep rising.
They expanded that evacuation order Thursday
, warning that levees will likely be overrun by Friday, putting even more homes in jeopardy.
Some bayous and creeks near Shreveport are expected to crest at levels not seen since 1991, according to CNN meteorologist Michael Guy.