Storm Boris proved deadly in Romania, where four people were killed during floods in the south-eastern region of Galati.
Sources said in the Czech Republic, flooding has led to evacuations and 51,000 households in the country’s northern areas have been hit by power outages.
Flood barriers have gone up in the capital Prague.
Poland also evacuated some people from Glucholazy, a town near the Czech border, after a river burst its banks.
The Romanian President Klaus Iohannis said they are again facing the effects of climate change, which are increasingly present on the European continent, with dramatic consequences.
Extreme precipitation is becoming more likely in Europe, as across much of the world, due to climate change.
A warmer atmosphere can hold more moisture, which can lead to heavier rainfall.
The mayor of Slobozia Conachi, a village in Romania’s Galati region, said 700 homes had been flooded.
Glucholazy resident Piotr Jakubiec said he had prepared sandbags and pumps to divert the water but that it was impossible to predict what’s going to happen.
Another resident, Zofia Owsiaka, said everyone in the town was scared and there seemed to be “no hope of the rain stopping.
In the city of Wroclaw thousands of residents had to use the staircases of high-rise blocks because lifts were shut as a flood safety precaution, local media reported.
Czech Prime Minister Petr Fiala said the country braced for a tough weekend. Authorities have put up protective walls of sandbags and metal barriers.
Football matches in the country’s top two leagues scheduled for this weekend were cancelled.