Bad Floods in Prague - Can it recover before end of June?

It can and probably will be gone by the end of June. Flooding is a seasonal hazard around rivers, these are just much worse than they have had in a few decades. Contact your lodging to see if they have been affected. If so, you should book nearby. If not, avoiding the area strains the local economy in a time when they really need your support. For me the silver lining is others will probably rebook to avoid Prague. I see it as a rare opportunity to see Prague when it's not packed (and when the locals actually appreciate the tourists who are there).

Thank you for your response. It seems like Venice is used to this, but I remember going to Jamaica and they couldn't fix a road that was damaged after 3 years. Since I don't have experience with Prague, your comment is very helpful and reassuring.

And just note, not all of Prague was hit, just some of the low lying areas near the river. I forget the name of that little neighborhood right by Charles Bridge on the Castle side of the river, but that looks like the worst area hit. From what I understand, the Old Town is fine. Now, if you were going to Passau, that would be a different story.

The worst is already over. It's not as bad as it was in 2002. By the time you will get there metro (subway) will be already open. This time (unlike 2002) it was not flooded only preventively closed. However beautiful neighborhood Kampa next to Charles Bridge on Mala Strana side was flooded (among other non touristy neighborhoods).

Found out my hotel is unaffected. Thanks all