If you were planning on visiting Heidelberg, or along the Danube this week, you might want to change your plans. The Neckar is flooding badly, and a lot of the old town area in Heidelberg along the river banks, is now under water. Much of the access to the Danube is also being affected by this. Check local sources for more information. The Main is also beginning to flood and overflow its' banks, but nothing serious so far.
Photos from the flooding in Austria. This does not look good. Salzburg especially. Trains have been stopped, and the Donau is at a 30 year high right now. http://orf.at/stories/2185316/2185299/
The Danube is now about 10 meters over its' banks. A train has derailed in Tirol and the entire area has been declared a catastrophe. Article is in German, but photos and videos are sad to see. http://kurier.at/chronik/oesterreich/hochwasser-und-starkregen-hundertjaehrliche-rekord-flut-in-oesterreich/14.465.194
I cross the Danube every morning on my way to work. Today, for the first time in the 10 years since I've been here, the Danube has overflowed its banks. The walking paths on either side of the river are under water! It doesn't effect downtown Vienna, but it is something I've never seen before.
This info was just posted on Trip Advisor from someone who lives in Munich: Munich City has escaped the worst of the rain and flooding and is fully open for business but some of the tourist areas where you may think of making a day trip to are currently badly affected. Here's a brief overview (as of midday 3rd June) as most up to date information is only in German: Rail: the line between Munich and Salzburg is flooded so there are no trains to there or Vienna or Berchtesgaden. There are also no trains running between Munich and Innsbruck via Kufstein or Mittenwald nor to and from Italy. The Frankfurt-Vienna line is also closed from Passau onwards meaning there are no trains from Germany to mid and eastern Austria at all on any crossing. Road, there's many B roads blocked by flooding or landslides in the region south and east of Munich but the most major blockage is of the Autobahn A8 between Munich and Salzburg which is completely flooded and closed. The flood water is still rising so it'll be a number of days before things settle down again.
Additional info from the Munich Trip Advisor poster:
Ok, I've just been to Munich station and there are now trains to Vienna/ Budapest which do not stop in salzburg but are routed on an alternative path. So thats some good news. Regarding Garmisch-Partenkirchen, the line north of Tutzing is now closed so theres a replacement bus service now in place from Tutzing and you must get the S-Bahn to Tutzing to get the shuttle as the regional trains have been cancelled. Theres no indications on when things will return to normal as that will only become apparant when the damage is visible to the line which is currently underwater, not forgetting that signals and other electronics may also be damaged by the flooding. The police reckon that the A8 motorway will remain closed until at least Thursday due to damage that would need to be repaired so you would presume that the railway would be in a similar position. Regarding Switzerland, that's to the west of the affected area, so from Mannheim to Switzerland theres no problems. The badly affected area is the area EAST and also SOUTH of Munich between the city hinterland and the Austrian Border. Theres also problems north east of Munich in the area bordering the Czech Border but nothing like the chaos between Munich and Salzburg that is just unprecedented.
I see at Spiegel Online that Passau was hard hit by the convergence of three rivers. Much of the town now stands under water. We just visited there in December. It looks pretty sad. http://www.spiegel.de/international/germany/flooding-worsening-in-parts-of-germany-6-dead-in-europe-so-far-a-903396.html