Your concerns are justified but the main compartment is designed to contain suspect water. If you're still concerned, run a 32 to 1, water to bleach solution through it followed by a liter or two of clean water. From Ray. I just returned from doing a 16 day trek in Nepal. Our outfitter used 2 Base Camps. They love them, but also supplement them with Katadyn Micropur tablets if they suspect their water is below human feces and thus possibly contaminated with dangerous viruses. First they filter,then add one Micropur tablet per liter of water. Since the filter has taken out hard to kill protozoa (plus all bacteria), the remaining viruses are killed in 15 minutes. No chlorine or iodine taste either. I'll admit that chlorine bleach would also work, but I don't like carrying bleach, measuring bleach, pouring bleach, or tasting bleach. thanks, Ray