France’s second city has been lashed by heavy rain in recent days and the state weather service, France Meteo, heightened an existing alert ahead of more forecast wind and rain.
President Jacques Chirac flew over the region and briefly visited a crisis coordination centre to express his solidarity with the 7,000 police, firemen and soldiers deployed and sympathy for the victims.
The government announced it was giving 12 million euros ($A19.74 million) in emergency relief for the disaster.
The central square of Montpellier was underwater, with just the tops of park benches visible and the empty main street inundated up to the doors of shops.
Cars were left abandoned in the torrents that had formed over other roads. Army trucks were used to transport people whose homes had been flooded.
Road and rail traffic in southern France have been severely disrupted, with many routes submerged, while more than 9,000 people living close to swollen waterways have been evacuated and tapwater was declared too contaminated to drink.
The reactors in two power plants were shut down because of floating debris in the river that threatened to clog cooling inlets.
Authorities updated their casualty toll Wednesday, saying five people had drowned.
The disaster recalled floods last year in the same part of France that killed 24 people.
It also tested the reactions of government officials who had been taken to task for their perceived mishandling of an August heatwave that cost the lives of 15,000 people.
Local authorities said the Rhone river, which runs from Lyon, in the southeast of France, to Marseille, was channelling a huge amount of water – 12,000 tonnes a second –and was at a dangerous level.
France Meteo said the river was overflowing under the heaviest rainfall seen in the region in half a century.