There were heavy storms in the two regions of Gard and Hérault on Friday morning and they were expected to hit the Drôme and Ardèche later in the day with hail feared.
The storms should ease off on Saturday morning but heavy rain was forecast to return on Saturday night.
The Hérault region and its main city, Montpellier, have been placed on orange alert because of the risk of flooding by the river Lez.
Six people have died and 4,000 forced out of their homes by storms that have hit southern France since September.
Montpellier has suffered the most from the flooding.