Tensions eased in cities upriver along the Elbe and its tributaries, including Dresden, Halle and Bitterfeld, where many evacuation orders were lifted and people returned to start clearing out their mud-caked homes.
The water level in Magdeburg was higher than during "once-a-century" floods of 2002, local authorities said. Magdeburg lies downriver from where the Saale river spills into the Elbe, creating a water surge a record 40 kilometers (25 miles) long.
Further downstream, towns including Lauenburg and the village of Hitzacker in Lower Saxony were preparing for the peak to hit in coming days.
The rains severely swelled the Danube, hitting southern Germany, especially the city of Passau, which has moved from alert to clean-up mode.
Further east along the Danube, authorities said Budapest flood barriers were high enough to protect the capital, where the river was forecast to peak at 8.95 metres on Sunday.
"Budapest is not at risk of a catastrophe, the level is not expected to rise significantly," Mayor Istvan Tarlos said, adding that leaking dykes had been fixed.
Switzerland had so far been largely spared the havoc wreaked by the floods but at around 6:00 pm (1600 GMT) Sunday, violent rain and hail storms hit the western cantons of Vaud and Fribourg.
The downpour caused mudslides and floods that blocked roads and a railway and forced more than a dozen people to evacuate, police said. No one was injured.
In Germany, President Joachim Gauck visited flood-hit regions, where in vast areas only roofs and tree tops stick out of the water and the only access was by boat or helicopter.
"One cannot imagine how much remains to be dealt with," he said.
Adding to tensions was a threat to attack dykes from a group calling itself the "Germanophobic Flood Brigade". Aerial and ground surveillance had been stepped up, said Saxony-Anhalt state interior minister Holger Stahlknecht.
Ironically, the sun shone Sunday above most of Germany's flood zone, forcing the thousands packing sandbags to seek supplies of sun block and insect repellent.
But more rains were expected by Monday in Thuringia, Saxony and Bavaria, with as much as 50 liters per square meter expected within a few hours.
Chancellor Angela Merkel was planning a crisis meeting with state premiers on how to share the bill for the disaster -- estimated to hit tens of billions of euros -- the Leipziger Volkszeitung newspaper reported.
"We're dealing with a national catastrophe," Gerda Hasselfeldt, lawmaker for the conservative Christian Social Union, was quoted saying.
Despite the widespread damage, growth in Europe's biggest economy was unlikely to suffer much as a result, said a survey of leading economists by Die Welt daily.
"Absurdly, economies actually pick up after natural disasters because the property damage needs to be repaired," Deutsche Bank chief strategist Thomas Mayer said.