Austria, Germany and the Czech Republic sent in army units to help with rescue efforts after rains reached record levels in some areas yesterday, while hundreds of roads have been closed and rail services cut.
The banks of the mighty Danube River burst in one area in Germany, and dozens of towns were put on flood alert across a large swathe of central Europe.
In Austria, one person was killed and two were reported missing following landslides triggered by heavy rains that forced several hundred people from their homes, local authorities said.
But despite the heavy rains, around 10,000 Bayern Munich fans joined in celebrations for their team's historic treble win in the European, league and cup titles.
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In the Czech Republic, a man and woman were killed in Trebenice, just outside Prague, when their house collapsed, police said. At least four other people were missing.
Officials ordered the evacuation of around 1,800 people from the village of Stechovice.
The body of a man in his fifties was found last evening in the swollen waters of the Upa River, at Trutnov, 150 kilometres northeast of the capital, said police.
The government declared a state of emergency and released 12 million euros in disaster funds. Several hundred people had to be evacuated, as well as a hospital and the Prague Zoo.
"We will do everything to protect people's lives and health," said Prime Minister Petr Necas, announcing that 1,000 troops had been mobilised.
"Tonight and tomorrow will be critical."
Barriers have been erected along the banks of the Vltava River in Prague to prevent it from flooding, and the iconic Charles Bridge was closed.
The southern German town of Passau on the Austrian border was partly flooded when the Danube burst its banks.
Further downstream, Austrian towns including Linz and Melk were bracing for the worst, with some local authorities fearing a repeat of the record floods in 2002 that caused damage of up to 7.5 billion euros nationwide.