The River Seine in Paris is at its highest level for more than 30 years, with floods forcing close parts of the metro systems and major landmarks.
The Louvre and Orsay museums were shut while staff moved artworks to safety as flood levels climbed above 6m (18ft).
The Seine is set to reach as high as 6.5m and unlikely to recede over the weekend, with more downpours forecast.
At least 15 people have died across central Europe as heavy rainfall caused flooding from France to Ukraine.
While two people died in France, 10 were killed in southern Germany as several towns were devastated.
Two more fatalities were reported in Romania and one in Belgium. Austria, the Netherlands and Poland have also been affected.
Tens of thousands of people have been forced from their homes.
In Paris, the Cluny – La Sorbonne and St Michel metro stations were closed as a precaution while the river spilled onto the city’s streets.
Bridges were closed and non-emergency boats were banned from the Seine as its swelling forced the closure of museums, parks and cemeteries.
At the Louvre, curators scrambled to move 250,000 artworks to higher ground from basement storage areas at risk of inundation from what President Francoise Hollande called “exceptional flooding”.
French authorities have even taken initial steps to transfer the presidency and key ministries to secure areas, AP news agency reported.
France’s rainfall levels in May were the highest since 1873, but the crisis is eclipsed by the 1910 floods that saw Paris submerged for two months.
The river level peaked at 8.62m that year, and has since reached 7.1m in 1955 and 6.18m in 1982.
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