Austria and Germany sent in army units to help with rescue efforts after rains reached record levels in some areas, while hundreds of roads have been closed and rail services cut.
The banks of the mighty Danube river burst in one area in Germany while dozens of towns have been put on flood alert across a large swathe of central Europe.
In Austria, one person was killed and two people 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.
Also Read
In the Czech Republic, one woman was killed and at least three other people were missing.
Barriers have been erected along the banks of the Vltava river in Prague to prevent it from flooding and a state of emergency has been declared in about 50 towns and villages in the west of country.
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 (USD 9.7 billion) nationwide.
Rail services between the southern German city of Munich and Salzburg in Austria were brought to a halt, according to German train operator Deutsche Bahn.
Rail links were suspended due to landslides in many parts of Salzburg and Tyrol, Austrian Rail said, while a section of the motorway to Switzerland was closed because of flooding, as were smaller roads throughout the country.