Hundreds of 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 a swell of floodwater moves in from the south.
Both Germany and Austria are deploying their armies to help emergency services.
A man was killed by a landslide near Salzburg in Austria and two people have died in the Czech Republic.
The Czech government has declared a nationwide state of emergency.
The Czech deaths came after floodwaters destroyed flimsy country cottages. Two more people are missing in the country after their raft overturned on a swollen river.
Firemen in Czech Republic capital have been putting up metal flood barriers and volunteers filling sandbags as the River Vltava is due to reach peak levels in Prague some time on Monday morning.
Czech PM Petr Necas has called a special cabinet session to co-ordinate the emergency response.
Authorities believe the river in Prague will not reach the levels it did in 2002, when parts of the city were devastated, but will still be high enough to cause severe damage.
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 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.
Bavaria is not the only German state to be affected; towns and cities in Saxony, Thuringia and Baden-Wuerttemberg are also inundated.
The Munich-based newspaper Sueddeutsche Zeitung reports that the German army is to be deployed in Bavaria, Saxony and Thuringia to support the flood-affected areas.
German Chancellor Angela Merkel has discussed the floods in phone calls with the premiers of Bavaria and Saxony, the paper says.
Near the Austrian city of Salzburg a man was found dead after being swept away as he worked to clear a landslip.
Two further people are missing in the Salzburg area, according to Austrian media. A third is missing in Vorarlberg.
The Austrian army was called in to help civil authorities in the settlement of Taxenbach, south of Salzburg. Their main task was to clear landslides and make roads passable.
Parts of the Pinzgau region, which includes Taxenbach, have been declared a disaster zone.