Well, you can filter the water for pathogens and other biologic organisms, and you can boil whatever might make it through long enough that you can destroy those organisms as well. However, some organisms create toxins which can pass through filters and will not be destroyed by boiling.

There are some organisms that live in the heated pools in Yellowstone that I think would be pretty bad if you tried to ingest them. I think they can tolerate up to 180 degrees F or so, but boiling may be just a bit too much for them.

Pasteurizing may be the best disinfectant process going so far as using heat to sanitize water goes.