A storm warning was issued for the city for June 4 and 5.
Much of central Europe is awash – as deadly flooding claimed at least 12 lives this week and continued to drive thousands of people from their homes.
Germany struggled to tackle its worst floods in a decade, with the army being called in to help reinforce river defence systems.
Chancellor Angela Merkel visited the city of Passau, in the hard-hit Bavaria region in the southeast of the country on June 4.
She pledged 100 million euros of emergency aid to the area.
Meteorologists said the worst could be over for Passau, but warned that the central German city of Dresden could be one of the next to be hit.
Across the border in Austria, the situation remained critical.
Some parts of the country received two months-worth of rain in just a few days, pushing the Danube river close to peak level.