Parts of the old town of Passau in Bavaria are under water
Homes have been evacuated across southern Germany, the Czech Republic, Austria and Switzerland as rivers reach dangerously high levels.
The Czech capital Prague is on high alert as authorities fear a repeat of the catastrophic floods of August 2002.
The River Vltava has inundated towns and villages upstream of the capital, and one person is known to have died.
The German cities of Passau and Rosenheim have declared a state of emergency.
Authorities in Passau, which lies at the confluence of three rivers in Bavaria, say they expect the Danube to reach 10.5m by Sunday evening and have requested help from the German army.
The BBC's correspondent in Prague says firemen have been putting up metal flood barriers and volunteers filling sandbags as the Czech capital prepares for a swell of floodwater.
Prime Minister Petr Necas has called a special cabinet session to co-ordinate the emergency response.
The woman who died in the Czech Republic was killed when her cottage collapsed. Two more people are missing after their raft overturned on a swollen river.
At least four people have died or are missing due to the floods in Germany and Switzerland in recent days, according to the Associated Press.
Bavaria's flood alert service warns that the forecast of continuing heavy rain is likely to worsen the flooding affecting the Danube and the Inn, among other rivers in the area.
The Munich-based newspaper Sueddeutsche Zeitung reports that rivers in Saxony and Baden-Wuerttemberg, as well as in Bavaria, have burst their banks.
Bavaria's premier, Horst Seehofer, has discussed the floods with Chancellor Angela Merkel and has called a crisis meeting for Sunday afternoon, the paper reports.
In the Austrian city of Salzburg a man was found dead after being swept away as he worked on flood defences.
Two further people are missing in the Salzburg area, according to the Salzburger Nachrichten.
The Austrian army was called in to help civil authorities in the settlement of Taxenbach, south of Salzburg.