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.