Storm Boris proved deadly in Romania, where four people died in floods in the southeastern region of Galati.
In the Czech Republic, flooding led to evacuations, and 51,000 households in the country's northern regions were affected by power outages, Czech power company CEZ said. Flood barriers have been erected in the capital Prague.
Poland has also evacuated some people from Głuchołazy, a town near the Czech border, after a river burst its bed.
"Once again we are facing the effects of climate change, which are increasingly manifesting themselves on the European continent, with dramatic consequences," Romanian President Klaus Iohannis said on Saturday.
Extreme rainfall events are becoming more and more likely in Europe, as in much of the world, due to climate change.
A warmer atmosphere could hold more moisture, which could lead to heavier rainfall.
How climate change is worsening heatwaves, droughts, wildfires and floods
The mayor of Slobozia Conacci, a village in Romania's Galati region, said 700 houses were flooded.
"This is a disaster of great proportions. Firefighters are piling sandbags as residents are evacuated," said Emil Dragomir. in Głuchołazy, in the southwestern Polish district of Opole,
A similar effort is underway in Krakow, Poland's second-largest city, where residents are being offered sandbags for flood protection.
City resident Piotr Jakubiec said he had prepared sandbags and pumps to divert the water, but also that it was "impossible to predict what will happen".
"This is the second time in my life that I have seen such a phenomenon. It's a nightmare for the people who live here," he said.
Another resident, Zofia Oussiaka, said everyone in the town was scared and there seemed to be "no hope for the rain to stop".
In the city of Wroclaw, thousands of residents had to use the stairwells of high-rise blocks as lifts were closed as a flood precaution, local media reported.
On 14 September, a dam broke in the southern Bohemia region of the Czech Republic. Environment Minister Peter Hladik urged people in the worst-affected areas to prepare to leave their homes.
Hladik said the ground was saturated and rainwater was being held at the surface, increasing the risk of flash floods. Rain is expected in the Czech Republic until Tuesday (September 17), the minister said.
Czech Prime Minister Peter Fiala said the country was preparing for a "tough weekend". Authorities have erected protective walls of sandbags and metal barriers.
Football matches scheduled for this weekend in the country's top two leagues have been cancelled. | BGNES