River levels have risen quickly by about one meter, with the Weiße Regen River in the Bavarian Forest reaching the highest state of alert at Kötzting before midday.
Meanwhile the Danube River was expected to reach top alarm levels by evening near Passau. Water levels there are at their highest since 2002, broadcaster Bayerische Rundfunk reported. Residents there have surrounded their windows and doors with sandbags and wooden walls, the broadcaster said.
High water along Danube tributary the Inn River was also reported, and sections of the Isar River were also in danger of flooding, the environmental authority said.
Bavarian police reported flooded streets and cellars across the region, adding that many roads had been closed. The counties of Berchtesgaden and Traunstein were among the most heavily affected areas, they said.
Meanwhile fire fighters were busy pumping water out of waterlogged homes, securing embankments and removing fallen trees in many cities.
Regional train service between Ruhpolding and Traunstein has been suspended as water levels also overflow nearby banks, Bayerische Rundfunk reported.