One thing to keep in mind - "Any water is better than no water." I started fairly serious outdoor trips in SE Arizona some years ago, and I soon adopted the notion that however sick this water makes me, by the time that happens I will at least be able to return to town where I can be cured. This has worked just fine for me in the back country - industrial waste situations closer to civilization might be somewhat different.

Indifferent water can be boiled and that will take care of the pathogens, although it won't deal with toxins, etc. I have boiled for years and never regretted doing so.