Some years ago, during an archaeological project in Canyon de Chelly, we were forced to subsist on flood water which was "too thick to drink and too thin to plow." We would collect a quantity in a basin and let it settle overnight (at least), decant the upper clear fluid, and then boil. Once we established our system, it worked just fine, with no problems or illness.

We knew we had to deal with waste from both humans and livestock, but chemical contamination was trivial. This would not be the case in many areas currently.