You probably realize that 'environmentalism' is essentially a substitute-religion for a lot of people today, and being 'natural' is a form of religious expression for them. Careful analysis of the facts tends not to be an important part of how many people approach their religion.
What evidence I've been able to find suggest that these natural pools are not nearly as safe as chlorine pools, especially as the bather load increases. But "more risk" does NOT equal "much risk" -- a distinction that eludes even many educated people.
But my guess is the risk is still pretty low for these pools, if they aren't used commercially. After all, my family's (and my own) PERSONAL preference is swimming in the ocean, which is more risky than either these natural pools or chlorinated pools, not just from infection, but from the OTHER wildlife or from physical hazards.
Many discussions of health risk today ignore that the MAJOR avoidable risks for most people are things like over-eating, not enough exercise, cigarettes, and poor medical treatment, including nosocomial infections. Infections transmitted in pools, or chemical risks from pool treatment are MINOR risks by comparison.
The higher risk SERIOUS events around pools, including drownings, slips & falls, electrocution, diving injuries, etc. rather than chemical or infection events.

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