"Between 800 and 1,000 people" were evacuating mid-Sunday from homes along the banks of the Agly river in the Pyrenees-Orientales region, the government office there said.
The flooding was considered already more serious than deadly overflows in 1999 and "we are evacuating residents within 200 meters (yards) of either side of the river," the government said.
Another 391 people had already left their homes in Canet, Argeles-sur-Mer and Barcares, on the Mediterranean coast.
"I'm 42 and I've never seen anything like it," said Kristel Gregori, who lives in Argeles, near the Massane, a stream which often dries up, but has turned into a 20-metre wide deluge inundating dozens of parked cars.
Southern France has been hit by weeks of successive storms and flooding.
Four people died and two including an eight-year-old girl remained missing in southeastern France after violent storms on Thursday and Friday triggered flash flooding, uprooting trees and ripping off roofs.