As paramedicpete mentioned, I believe it simply has to do with resistance/tolerance. Back in the old days, all the water you drank came from the stream, well, or what-have-you. Many of them probably did get sick from the organisms a few times as a child. I’d imagine that after a few times of being sick, they would have developed a resistance to those particular organisms and therefore rarely got the same sickness again.

Now, if you compare that to today’s modern primary use EPA-controlled purified tap water and commercially-controlled purified bottled water, the chance to develop a resistance or tolerance to “nature’s flavoring” is nonexistent.

In fact, I imagine the same situation describes why water from other countries rarely agrees with us, too.