In southern Bavaria state on the Austrian border, firefighters and other emergency services were dispatched to inundated towns.
"The floods came so quickly that people had to escape to the roofs of their houses," a spokesman for the Lower Bavaria regional police said, adding that many streets were submerged.
The town of Triftern, around 200 schoolchildren bunked down in their school, preparing to spend the night, when road access became restricted. A town spokesman said the school building itself was out of danger as it was on higher ground.
Their group of 12 boats became separated in the raging current sparked by a sudden storm and panic broke out among the pupils.
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About 20 members of the group had to be rescued by emergency services, while the others were able to reach the riverbank on their own.
Just over the border in Austria, heavy rain lashed the Salzburg region, flooding several roads and forcing several schools to announce closures for tomorrow.
In Paris, many promenades along the Seine were closed due to high water while in Nemours, 80 kilometres (50 miles) to the south, residents had to be evacuated today afternoon after the Loing river burst its banks.
The neighbouring Loiret region saw the average rainfall of six weeks in just three days and Chambord, the Loire Valley's best-known Renaissance chateau and a tourist magnet, was surrounded by rising waters.