Native tribes would get sick from bad water all the time. It was a fact of life. But they also understood where to get water that was less likely to make you sick.
Fast moving streams and water are less likely to contain parasites and pollutants and native tribes understood that.
There was also a lot less pollutants in the water ways than there are today
Anyone who’s drank well water for a while also understands that it makes you sick at first, but you get used to it after a while. Your gut builds up a tolerance to what’s in the water and you are less likely to get sick.
A mixture of the obvious things you’re considering.
They would know, even if they didn’t understand the “why”, that certain bodies of water were safer to drink than others. A clear, cool, running stream would be safer than fetid stagnant water for example.
Many cultures did eventually figure out boiling the water or using it for fermentation would make it safer.
People also got sick, that was just a thing. Usually they got better, sometimes they died. But in general “being sorta sick” was just more normal back then, you just had larger proportions of the society on the DL at any given time in general.
Finally, there is some level of acquired immunity to certain illnesses and local people might just progressively get better at handling the local microbes.
We removed the forests and those forests were part of the natural filter system. Now we have crops everywhere that get tilled every year. This leads to agricultural runoff. These nutrients from the farms over-fertilize water bodies, basically making them cesspools for microbes. The Problem is, the biomass load is so high that the oxygen gets depleted. Dangerous microbes live in low oxygen conditions and these polluted waterways become a risk instead of a resource.
This pollution can be mitigated by 99% with one or both techniques names Keyline-Plowing, and or Permaculture-Swales. These landscaping techniques harvest water and stop erosion, turning the landscape into a natural filter again.
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