One thing I learned since scouts in the 60's about water/food in the backcounty is to "think!". Try and figure out the path that water took to your point and all it passed through.
Ag runnoff is hard to escape these days. My dad has a running spring in his back yard that is sourced by several thousand acres of farmland. Yuk...good for the yard but treatable only by distilling.
I did get guiarda as a teen while fishing in Mexico. Our bait was fresh shrimp and we had tons of it. At the end of the day, we boiled, then RINSED and ate it. I was sick for a month after I got home. It was the cool rinse water that got us.

Keeping food utensils safe is an interesting subject. Homeless people in the area, we learned, sterilize with heat. We don't see much food poisoning in that community.
While backpacking along the Rio Grande in Big Bend last week, I watched some Mexican cowboys "clean" their pans in the river...which is filthy, and has a high e-coli count. But they seem to handle it, since that's all they have available. I won't even wash my hands in that river!