Since Thursday, swathes of Austria, the Czech Republic, Hungary, Romania and Slovakia have been hit by high winds and unusually fierce rains.
"We are again facing the effects of climate change, which are increasingly present on the European continent, with dramatic consequences," Romania's President Klaus Iohannis said.
"We must continue to strengthen our capacity to anticipate extreme weather events."
In Romania, four bodies were discovered in the worst affected region, Galati in the southeast, where 5,000 homes were damaged.
Hundreds of people have been rescued across 19 parts of the country, rescue services said, releasing a video of flooded homes in a village by the Danube river.
"This is a catastrophe of epic proportions," said Emil Dragomir, mayor of Slobozia Conachi, a village in Galati, where he said 700 homes had been flooded.
Prime Minister Marcel Ciolacu is visiting the area, while President Iohannis sent his "condolences to grieving families".
Around 100,000 firefighters have been mobilised in the Czech Republic, where nearly 2,900 incidents were recorded on Friday, most of them due to fallen trees and floods.
Almost 50,000 homes were without electricity on Saturday, Czech power company CEZ said, and a hospital in the southeastern city of Brno was evacuated on Saturday morning.
"The ground is now saturated so all the rainwater is going to stay on the surface," Environment Minister Petr Hladik said on X, formerly Twitter.
In Austria, rail services were suspended in the country's east early Sunday and several metro lines were shut down in the capital Vienna, where the Wien river was threatening to overflow its banks, according to the APA news agency.
Emergency services had made nearly 5,000 interventions overnight in the state of Lower Austria, where flooding had trapped many residents in their homes.
- 'Everyone is scared' -
Neighbouring Slovakia has declared a state of emergency in the capital, Bratislava.
Meanwhile in Poland, the government warned the situation would be the most difficult in the southwest going into Saturday afternoon and evening.
Authorities have shut the Golkowice border crossing with the Czech Republic after a river flooded its banks, closed several roads and halted trains on the line linking the towns of Prudnik and Nysa.
In the nearby village of Glucholazy, Zofia Owsiaka watched with fear as the fast-flowing waters of the swollen Biala river surged past.
"Water is the most powerful force of nature. Everyone is scared," local resident Zofia Owsiaka, 65, told AFP.
"This is the second time in my life that I've seen such a phenomenon. It's a nightmare for the people who live here," added Piotr Jakubiec, 39.
Austria registered winds of 146 kilometres (91 miles) an hour in the south.
Firefighters have intervened around 150 times in the capital Vienna since Friday to clear roads blocked by storm debris and pump water from cellars, local media reported.
Four thousand homes in the Styria region are without power and the "peak is yet to come", Chancellor Karl Nehammer warned.
In mountainous areas of the west, snow halted traffic and rescue services were searching for a man reported missing after an avalanche.
Parts of northeast Austria have been declared a natural disaster area.
Some areas of the Tyrol were blanketed by up to a metre (three feet) of snow -- an exceptional situation for mid-September, which saw temperatures of up to 30 degrees Celsius (86 degrees Fahrenheit) last week.
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