National weather agency Météo France still had orange alerts in place, one step down from its maximum red alert, across ten southern departments on Friday morning.
Cities including Marseille, Montpellier and Lyon were all affected by the weather, which Météo France expects to worsen again on Friday evening.
In the Hérault region, 70 centimetres (27.5 inches) of rain fell in four days.
The river Hérault avoided bursting its banks and flooding the village of Laroque after rain eased overnight, although more is expected later in the day.
Elsewhere, people were evacuated from their homes as the danger of flooding increased.
A number of schools were closed across the region on Friday as transport was made impossible by flooded roads. Train services have also been disrupted and drivers have been warned to exercise "extreme caution."
France Télécom said in a statement it had mobilized 1,000 engineers to deal with network problems caused by the storms. The company said 4,000 lines had been cut off in the Languedoc-Roussillon region on Thursday.
Ecology minister Nathalie Kosciusko-Morizet said the storms were exceptional. She advised local residents to avoid driving or walking on flooded roads.