The country's Health Ministry warned of the spread of waterborne diseases owing to flooding disrupting water supplies and flushing raw sewage on to the streets.
"People aren't frightened but they are anxious with many of them going down to look at the river," said Michael Prochazka, a Prague local. "We don't really know when it's going to peak so who knows what will happen."
The Czech regions of Bohemia and Moravia suffered severe damage from the flooding, especially in mountainous areas where narrow valleys funnelled the destructive force of the water. In Germany, the Government deployed 1760 soldiers as flood waters engulfed the centre of the southern city of Passau, passing the previous high-water mark set by floods in 1954.
Further south, the cities of Bratislava and Budapest braced themselves as flood waters made their way down the swollen Danube. In Poland, dozens of towns went on alert as water levels on rivers flowing from the Czech Republic began to rise.
The flooding is the worst to strike the Czech Republic since 2002, when rivers burst their banks and caused damage estimated at millions of pounds.