With the new awareness of brain-eating bacteria and other parasites, is it safe or adviseable to swim in untreated creek water or spring water?

I used to get severe ear infections from swimming in untreated water, such as the Tennessee River or horseplay with canoes and paddle boats, causing capsization.

Covertly, I’ve always liked the idea of a water feature for swimming that used a well pump or artesian well source, or a natural spring.

I’ve heard of at least once case of brain-eating bacteria infesting victims at a spring-fed waterpark.

So, can a natural, untreated water source ever safe from bacteria and parasites? Must we always swim in treated water?