I was hoping (perhaps in vain) that "chlorinating the pools" was just tongue-in-cheek humor. So help me out here, is this guy serious or not? If one were to chlorinate the pools where that chlorine would surely run off into the creek would be to invite ecological disaster. What if the bacteria are breeding underground where the water is heated? Then chlorinating would do no good. And that's assuming the problem is bacterial in the first place.
Having the water tested is the correct first step but something tells me that that will not be inexpensive. Perhaps this is something the Forest Service could be asked to check into however then you do risk their increased scrutiny of the area. But let them get wind that someone is planning on dumping jugs of chlorine in the pools and they'll shut the area down for sure.
Any corrective measures taken should be done in consultation with an ecologist and, if necessary, a microbiologist. Please, no "vigilante" cures!