It is believe to be the worst flooding in the area since 1891.
Interior Ministry spokesman Frederic de Lanouvelle said one other person is missing and five others are seriously hurt.
He said nine of the 13 dead were clustered in one town, Trebes, in the Aude region, and that the number of dead could increase.
The flash floods swamped a number of towns and villages around the fortress city of Carcassonne, leaving a trail of overturned cars, damaged roads and collapsed homes.
BFM TV said one victim, an elderly nun, was swept away by flood waters, and two people who had been reported missing were found dead.
SKY News.
