When I go into the Sierras I never filter the water. Twice I got hit and probably mildly other times. I have a regimen I use. Zinc capsules, garlic oil, probiotics and activated charcoal. Aloe vera juice/gel will also help ingested. Don't take too much.
The amino acid L-Glutamine is also very helpful. Not enough fiber is the root cause of many GI tract problems.