About 4,000 people were stranded in the Hérault department, which was on red alert Tuesday morning, while the neighbouring Aude, Gard and Pyrénées-Orientale were on orange alert.
The government was set to declare a natural catastrophe in the Hérault, which was worst hit.
After a brief respite, the deluge was expected to start again as rain moved up the coast from Spain.
Hundreds of rail passengers spent the night sleeping in Montpellier’s railway station, some in carriages provided by the rail company, 500 people were stuck overnight in the airport, a concert hall was transformed into a dormitory and about 1,000 students had to sleep their schools and colleges.
The Red Cross and the army supplied camp beds and meals and the more than 1,500 firefighters and police who were mobilised for rescue efforts were called out 1,200 times.
Traffic was brought to a standstill by floods in the city streets as the River Lez burst its bankd on Monday afternoon and one intrepid resident rowed a kayak down a street near the old town.
Rainfall reaching 300mm in some places led to waterlogged soil in much of the area, leading the authorities to maintain the red alert ahead of the expected new downfall.
Ten days ago four people died in nearby Lamalou-les-Bains and another in the Aveyron.