For those travelling right now to the area, consider that extensive floods have been pouring down Garmisch-Parternkirchen, Salzburg, Passau and other cities on the area. It is an ongoing situation ensuing cancellation of many trains, flights and interrupting several road connections including some Autobahnen. So triple check and keep updated if your travel plans include that area next 24/48h .
There are also floods in western part of Czech Republic (Bohemia). Government announced state of emergency. Many stations of Prague subway are closed. Hospitals being evacuated, Prague ZOO, too. Lot of roads are impassable, train station in Kolin is under water (it's on the way to Kutna Hora, Brno, Olomouc, Bratislava, Wien, Budapest, etc.).
All, Also, Major portions of Rhine and Danube closed to boat and ferry traffic now. Triple check any travel plans for sure.
The Danube is extremely high. Melk and many towns, villages, badly flooded.
It's actually Bohemia and the surrounding countries. In Germany not only Bavaria is affected but also Thuringia, Saxony and Saxony-Anhalt. Here is a map: Click me
Yes, all this water will ultimately flow to the Rhine or Danube. High water alerts are in place for Netherlands, most boat traffic on the Rhein-Maas delta will shut down as waters raise.
I drove down to Oberwesel and Bacharach today to have a look. B9 and B42 (the two roads that run along the Mittelrhein) are both closed to traffic and submerged at various points along the way. The towns are still accessible by rail, however, and you can drive to them from higher elevation. You just can't drive all the way along the Rhine like usual. The little area of parkland on the riverfront of Bacharach is flooded, but most of the town appears to be as normal. All river traffic seems to have stopped temporarily.