The odds of a healthy individual becoming ill from drinking water in pristine wilderness is actually extremely low. There is really no evidence for your assertion that you will automatically become ill from drinking unfiltered water once. My understanding is there is little risk if the water is not under upstream human or livestock use.
http://www.wemjournal.org/wmsonline/?request=get-document...
Very few people in the “middle ages” lived in pristine wilderness. The vast majority were, and always have been, rural peasants in feudal or semi-feudal societies, working as serfs or sharecroppers or slaves, either on tiny individual plots, or on plantations. They became ill constantly, and most children died before age 5. You seem to be imagining some kind of hunter-gatherer society.
