Swollen rivers in the German states of Saxony-Anhalt and Schleswig-Holstein posed the biggest threat after flood waters caused billions of euros in damage and left at least 19 people dead across Europe.
Two burst dykes on Monday alleviated some of the pressure on other fortifications up the Elbe River but around 9,000 soldiers were deployed in Saxony-Anhalt in the centre of the country to ensure they held.
And in Schleswig-Holstein in the north, fears focused on the town of Lauenburg, 40 kilometres (25 miles) southeast of Hamburg, where the Elbe was expected to peak on Thursday.
There the river has already reached a level of 9.56 metres, more than double the normal. The old quarter of the town saw its power cut and some 400 people had to be evacuated.
Downriver the Elbe stabilised as towns and cities remained in a state of alert, particularly in Magdeburg, the capital of Saxony-Anhalt, where more than 20,000 have had to seek emergency shelter.
Meanwhile Hungarians breathed a sigh of relief as the level of the Danube continued to fall, to 8.59 metres at 0500 GMT Tuesday from 8.81 metres on Monday.
Travel restrictions in Budapest were expected to remain in place for another week but a key bridge linking Hungary to Slovakia reopened to traffic.
Chancellor Angela Merkel made her third trip to the German disaster region on Monday and praised the "impressive" work of volunteers to keep the muddy waters at bay.
Economy Minister Philipp Rösler said Tuesday the government would establish an aid fund for stricken residents and businesses using a model established after "worst-in-a-century" floods in 2002.
"That was a success," he told Berlin's Inforadio, saying the amount of the new fund would be determined after the floods had passed and the cost of the damage had been tallied.
He had told rolling news channel NTV on Monday that those affected could expect a payout of 50 percent of their assessed damage.
Merkel, who is just over three months away from a general election, is to meet Germany's 16 state leaders Thursday to discuss recovery efforts.
Meanwhile a staple of the German diet, the potato, looked to be another victim of the flooding as the fruit and vegetable industry association (BOGK) warned that a meagre harvest could drive up prices.
"It is not unlikely that there could be a shortage of French fries, dumplings and chips," BOGK managing director Horst-Peter Karos told the daily Bild.