A bit of both.
*Generally* clear, moving water is going to be safe to drink.
Boiling and filtering water was also very common.
And your immune system handles the minor funky bits that might make it through. Now when people moved to different locations where the water might have different pathogens, then it could cause an issue. Traveler’s Diarrhea was a thing even in ancient times.
And of course the unfortunate nature is that many people just died. Diseases like Dysentery were quite common.
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