Does Noah's flood count? If so, you have a lot to choose from....

I'm going to assume you don't want those. I took the simple expedient of searching the Traditional Ballad Index for songs with the keyword "flood," then tried to take out the Noah songs, and got this list (the ones marked * seem to be historical):

* The Alabama Flood
Annan Water
* Backwater Blues
* The Brushy Mountain Freshet
* Cairo (II)
* The D & H Canal
* The Galveston Storm
* The Great American Flood Disaster
* The Johnstown Flood (I) [Laws G14]
* The Johnstown Flood (II)
* Mighty Mississippi
* Mississippi Heavy Water Blues
* Shawneetown Flood
Waterbound

A lot of those are about the Mississippi Flood, but we also have Johnstown, and Galveston, and some less-well-known ones.