The Gard region, where firefighters reported the missing person, was on red alert after as much as 350 millimetres (13.5 inches) of rain fell in parts of the Cevennes mountain range on the edge of the Massif Central.
A similar amount cut off 10 departmental roads in the Gard, among them one in the Pont-d'Herault municipality, with prefectural sources indicating one village was isolated as a result.
Helicopters carried out two rescue missions and some 650 rescue personnel were mobilised for three further operations as some 200 people were led to safety in two villages.
Regional sub-prefect Jean Rampn told AFP that all people at risk had been moved to more secure areas.
Regional fire brigade spokesman Eric Agrinier told BFMTV that some people had reported seeing the vehicle of the missing person, a 64-year-old woman, swept away in a strong current.
The mayor of one commune, Anduze, some 70 kilometres (45 miles) north of Montpellier, told AFP around 100 houses on low ground had had to be evacuated.
She added that two local schools had been opened to provide overnight shelter as yet more rain, foretast to last until the early hours before moving further east, cascaded down across the late evening.
A man walks down a rain-soaked street in Anduze, southern France. Photo: Nicolas Tucat/AFP
Valleraugue, a village to the west of Anduze, saw 200 people forced to take shelter after local officials reported 45 centimetres of rain fell in 12 hours.
The commune saw 98 centimetres over just 10 hours in an even worse downpour in 1900.
Interior Minister Gerald Darmanin said he would visit the region Sunday afternoon along with Barbara Pompili, minister for ecological transition.
The adjacent Herault department was also hit by severe storms.
Heavy rainfall had blocked several roads from the early hours, prompting local authorities to urge people to stay at home.