Officials across central Europe issued disaster warnings and scrambled to reinforce flood defences as rivers threatened to burst their banks after days of heavy rain.
Several people have died or are missing in the floods in Germany, the Czech Republic and Switzerland since Thursday.
Some residents also have been evacuated from flooding in south-western Poland.
Czech officials said the waters of the Vltava river could reach critical levels in Prague and that special metal walls were being erected to prevent flooding.
Interim Mayor Tomas Hudecek said they were shutting down eight stations of the capital's subway network and urging people not to travel to city.
Anticipating traffic problems, the mayor said all nursery, elementary and secondary schools in the Czech capital will be closed today.
In the nearby town of Trebenice where a woman was found dead in the rubble after a summer cottage collapsed due to the raging water, authorities discovered the dead body of a man. Separately, at least three other people were reportedly missing. Many roads and train lines were closed, including a major one from Prague to the eastern part of the country.
Czech Prime Minister Petr Necas said 300 soldiers have been deployed to help local authorities and that up to 2,000 have placed on standby.
The government also declared a state of emergency in six regions, in the western half of the country and Prague, that have been badly hit by the flooding.
Thousands of people have had to be evacuated from their homes across the country, mainly in the north and the south.