The Seine, the Rhone, the Saone and their tributaries have all overflowed, while the Rhine appears to be receding, according to monitors.
In Paris, the Seine was 5.24 meters above the bridge d'Austerlitz at 13h in the southeast of Paris, and is rising two centimeters per hour since morning, according to the last meter reading
The Zouave Bridge Alma, the stone statue used as a popular landmark for assessing water levels, has water up to the knees.
Water retaining barriers were fitted in the 12th, 15th and 16th districts, according to the city hall, which has also asked Parisians "not to store valuables in cellars and basements ".
Roads on banks, gardens and undergrounds at the edge of Seine remain closed, while all river traffic upstream of Suresnes has been halted.
Seven Parisian stations of the urban rail line that runs through Paris, the RER C, that runs form
Boulainvilliers in Saint-Michel, have also been closed as has Metro line 7, which runs along the banks of the Seine.
Ski resort shut down
Meanwhile, in Strasbourg, regional authorities announced they were opening an emergency containment zone to stop the Rhine overflowing after days of snow and heavy downpours.
The 600-hectare polder at Erstein near the German border was evacuated Monday and can take in up to 7.8 million cubic metres of water diverted from the massive river, authorities said.
Further along the border, the medieval Swiss town of St Ursanne has been transformed into a lake, images on RTS television showed, while several mountain train lines have been halted.
A mudslide caused a Swiss regional train in Solothurn to derail late Monday, although there were no injuries.
French flood agency Vigicrues warned people on the risk of power cuts, saying "even areas that rarely flood" could be inundated.
In the eastern town of Ornans, home to 4,000 people, the high street was flooded and the ground floor of the town hall underwater.
"We haven't seen a flood like this since 2002," mayor Sylvain Ducret said.
Rains were continuing to lash swathes of France, with schools in the Alpine region of Isere shut Tuesday after heavy snowfalls.
The popular ski resort of Chamonix closed its pistes, with around 100 chalets evacuated over fears of an avalanche.
"This situation is out of the ordinary," said local mayor Eric Fournier.
"A level of snow usually seen in five months has fallen in 45 days. At high altitudes, we only see snowfall of this amplitude every 15 years."