I think we all know nothing is always 100% effective when it comes to sanitation. Fortunately, mere exposure to these organisms isn't always clinically significant. It generally takes more than a single cyst or bacterium entering your gut to make you sick. It may take hundreds, or more, and even then you may still not get sick. The object here is to reduce your odds as much as you can.

General sanitation also plays a part. A large percentage of supposed back-country gastrointestinal "waterborne illness" is most likely fecal-oral or other types of infection by routes involving the hands, cook wear, water bottles, clothing, foodstuffs, etc., and not the water supply.

I either don't worry about it overmuch, and trust my luck and iodine crystals or filter, or I double up and use both when I am feeling doubtful about my water source. I also try to let the iodine work overnight, for maximum contact time, then filter it. I have a large "dirty water" bag for this, then I filter it directly into my water bladder and bottles.

For anyone who is interested in really safe water, here is what our DMAT team uses:

Jeff