If you really want good water, be prepared to boil. I either do that or use a Pur Hiker, which will take care of just about everything except viruses, which we are told are not to be found in waters in the United States. Boiling has worked for me with water coming from streams running through active cow pastures and other noxious sources.

In one extreme situation, I just let the muddy water settle for a day after boiling and then decanted the clear liquid at the top of the container. We were camped for an extended period at one locality (archaeological site), but the water was contaminated with sheep and human waste. We had no problems whatever after a three week stay.