Tens of thousands of Germans, Hungarians and Czechs were evacuated from their homes after the region's worst floods in a decade.
The deluge has killed at least 12 people in central Europe since the weekend.
Water started subsiding in Prague and Passau, but fears grew for Bratislava, Budapest and parts of Germany, which forecasters said would be hit in the next few days.
About 1000 people had to leave homes in the German city of Dresden. Further north, authorities in the town of Halle on the Saale told hundreds to leave their homes. German Chancellor Angela Merkel has promised £850,000 in aid.
Water receded in Prague, although the medieval Charles Bridge remained closed. Floods spread to low-lying northern areas of the Czech Republic near the industrial city of Usti nad Labem. About 3700 people were rescued.
A barrier broke at the Lovochemie chemical plant in Lovosice, north of Prague, flooding the factory. Workers and dangerous substances had been moved.
Czech emergency services said they rescued 19,000 and the government freed up millions for flood repairs.
In the Slovak capital Bratislava, parks and a waterfront Danube cafe were flooded. In Budapest, 1200 people piled up sandbags and roads were closed near the Danube.
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