Several roads can only be passed by boat and a dozen or so schools have closed.
Vigicrues, the agency that monitors and warns of floods in France, describes the floods as “exceptional”.
At least seven people have been injured and 1,500 firefighters have been deployed to the region to help, writes Interior Minister Gerald Darmanin on X, formerly Twitter.
Red warning will be in effect until Wednesday evening.
Several weather warnings have also been issued in northern Italy. In Liguria, a regional state of emergency will be declared, Ansa reports.
Both France and Italy are still recovering from storm Ciaran, which swept across western Europe last week.