The "Herminia" depression has unleashed downpours especially in the Ille-et-Vilaine department, with administrative centre Rennes experiencing its worst flooding in 40 years.
Weather service Meteo France warned that the situation could get worse.
Eight other French departments were on orange weather alert for flooding, flash floods or, in the case of the French Alps, avalanches.
"Unfortunately we haven't seen the worst of the flooding," the mayor of Rennes, Nathalie Appere, said late Sunday.
"Water levels will not begin to subside slowly until Wednesday."
The city over the weekend evacuated some 400 residents living in streets near the city's Saint-Martin canal, and turned gyms into temporary shelters.
The rising water lifted houseboats on the canal to the same level as cars parked in the street.
Brittany's western-most area Finistere was on orange flash flood alert Monday, a level that was to be widened to the entire west coast on Tuesday, Meteo France said.
Herminia, which brought on the heavy weather over western France, follows Storm Eowyn which hit Ireland and the United Kingdom before the weekend.
Its impact on France's northwestern regions was exacerbated by the fact that the ground was already drenched from previous persistent rainfall.
Authorities have warned of difficult road conditions across the region, and disruption of rail services.
Scientists have shown that climate change caused by humans burning fossil fuels is making storms more severe, super-charged by warmer oceans.
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