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Did the contacts really make a difference here or is swimming in affected waters the main hazard?
My understanding is that acanthamoeba are basically everywhere, and the contacts being worn when swimming or showering are actually one of the main factors in acanthamoeba infection. They normally eat bacteria but they are opportunistic parasites, and I guess the contact gives them the opportunity.
So does the acanthamoeba get stuck behind the contact and can't get washed away by tears? Or do the contacts cause small abrasions that serve as an entry point? What role is the contact lens playing?
I'm only a student in the field so NotADoctor™ but under normal conditions your tear film layer and blinking keep other liquids out of your eyes. When wearing contacts in water or when cleaning them with tapwater, there is a small amount of the fluid that gets trapped against the eye. If that fluid is fresh water contaminated with acanthamoeba, it provides ample opportunity and time for the acanthamoeba to break through the layer and the contact lens prevents it from being blinked away.
Probably didn't help, but yea...infected water and getting it in your eyes and not rinsing them properly really doesn't help.
I'd imagine tearing and blinking may rinse them away before they could burrow, but if they got under the lense they'd be protected.