Five people are believed to have died and a state of emergency has been declared in parts of the Czech Republic.
The river Elbe continued to rise and authorities warned that thousands may have to flee the town of Melnik, 30 kilometres north of Prague, where the Elbe and Vltava rivers meet.
In Germany, 300 people have been evacuated from Dresden, where the Elbe threatened to flood the historic city centre.
Floods in Hungary had disrupted road and rail services in several parts of country with 350 people evacuated from homes near the Danube.