"It's peaking in Prague right now and by the evening the wave will get to Usti and Labem," about 30 kilometres up the Elbe river from the German border, Petr Dvorak, spokesman for the Czech Hydrometeorogical Institute, told AFP.
The floods have deluged Prague's historic centre, shuttering businesses and forcing a chaotic nighttime evacuation of the city's zoo.
The floods have killed seven people so far in the Czech Republic, police said today. Two people died in Austria and one in Switzerland. Germany has also been hit.
Fire brigades evacuated 8,340 people as of 0930 IST today, said spokeswoman Nicole Zaoralova.
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The heavy rainfall has triggered nightmarish memories of the 2002 floods that killed dozens in the region including 17 in the Czech Republic alone.
Dvorak said the waters would recede in the western part of the Czech Republic tomorrow.
"There will be heavier rain in the east of the country and some rivers there will rise high, but the extent should be lower than here," he added.