A state of emergency has been declared in the Czech Republic where hundreds of homes have had to be evacuated due to flooding.
More heavy rain is forecast.
High water levels in Prague triggered the closure of flood protection gates.
The village of Minisek is submerged after river levels rose by up to four metres.
Many houses are said by the authorities to have been irreparably damaged and will have to be demolished.
Rescue services are searching for anyone who may still be stranded by the rising waters.
Heavy downpours have also caused flooding in Chemnitz in Germany’s Saxony forcing the closure of the region’s main highway.
While in southern Germany more than 100 litres of rain per square metre fell in 24 hours in the Allgau mountain range in the Bavarian Alps.
In Poland a sudden storm flooded homes, roads and hospitals and forced the closure of several underground stations in the capital Warsaw.
Emergency services had to rescue passengers on a bus stuck on a flooded road in the city.
Polish media has been reporting high winds uprooting trees and ripping off the roof of at least one building.
Firefighters have been struggling to cope with more than 1,500 emergency calls from people whose homes have been hit by the deluge.
Heavy rains are also reported in Spain, Italy, Austria, Slovenia and Serbia.