Cholera outbreaks are common in flood situations, and are notoriously difficult to contain. I suspect even after they're removed, a great number of the refugees will probably end up in little "bushvilles" (anyone here enough of a history buff to remember 'hoovervilles'?) where they can keep a lid on infectuous disease outbreaks and, presumably, try to figure out something to help these hundreds of thousands get back into living a life.
Needless to say that the life of a refugee will be made marginally better by being in, say, a tent with daily water and MREs, but for many of the poor that will likely be bulk of their existance for a very, very long time.
