Sure, they knew drinking something gross was likely to make you sick. If your nice clear river is downstream from a public lavatory, would they see a problem with that, though? Probably, they’d only worry if it was close. Bad smells and weird sounds (like got Bach in trouble) are similarly mentioned as sources of disease.

As for alcohol, I should point out it has the effect of alcohol, and getting drunk is popular. If it was about safety, making a nice herbal tea (or actual tea if available) is easier and faster and much more effective at killing bugs.