That's a good question. To the best of my knowledge, all the crap that makes us sick tends to be either the organism, or a toxin made by it. Most toxins tend to be proteins, so I assume if you boil, you'll denature it and the protein will be rendered inert. But I've also heard that spores and prions are pretty robust. I wonder about them? I'll see if I can corner one of the microbiology professors in campus this week and give you a professional opinion!

I tend to agree with Silent Weapon: better to drink than dehydrate and die. After all, my dog drinks water from anywhere, and she's still around. You figure organisms have been dealing with the water on the planet a few billion years (if you believe in evolution), so I'm sure we can survive it still, generally speaking.