Legions of soldiers and volunteers worked through the night to reinforce dykes and repair leaks in both eastern Germany and in Hungary.
Throughout the German state of Saxony-Anhalt, thousands of residents have been evacuated from their homes as water levels on the Elbe river - already at record levels in the past few days - continued to rise by some two centimetres (0.8 inches) every two hours, according to officials.
In Bitterfeld, patients had to be removed from a hospital as a dyke threatened to burst, and in the nearby medieval city of Magdeburg, flooded roads forced the evacuations of several old people's homes.
The mayor of Magdeburg Lutz Trümper said he fears what could be a "dramatic weekend" and said the town could face "the worst flood in its history."
In Mühlberg, a town in Brandenburg state that was already evacuated in the last few days, the situation remained "very tense," said local police spokeswoman Ines Filohn.
Some 900 soldiers and volunteers overnight there had to build an emergency road so hundreds of trucks could gain easier access to a dyke that needed to be reinforced.
"We need to protect the dykes no matter what," said Wolfgang Brandt, a spokesman of the Brandenburg state crisis centre.
Along the Danube, Hungary was next in line to suffer from the rising waters, with the flood expected to peak on Monday morning in Budapest.
Meanwhile, the bridge linking Slovakia and Hungary at Esztergom was closed to traffic early Saturday.
In the Czech Republic, the clean-up effort was under way to remove the thick layer of muck left behind by the retreating waters, but Prime Minister Petr Necas warned that "the floods are not over."
With more heavy rains expected in the next few days, the soaked ground would not be able to absorb any more water and anti-flood precautions were to stay in place, according to the authorities.
Meteorologists in western Austria, one of the first regions hit by the floods last weekend, also warned that new rain in the coming days could trigger more flooding and landslides in the alpine valleys.