There is always some possibility we can pick up a harmful pathogen in everything we eat, drink or touch. It's just not something I care to worry about. I try to filter all my drinking water but am not afraid to drink unfiltered running water in the mountains if I have to. Do your homework before a trip. I know of springs that even have naturally occuring arsenic in them (not mining related). These are usually well know by the rangers and guide books as well as the locals. Check before you go.
When I was twelve, a parent hauled us up to the mouth of a canyon near here. Three of us packed in 3 or 4 miles, set up camp, drank plenty of the water we were going to fish in the next day. The second day we fished downstream, came back that evening, drank more of the water, washed in it, cooked our food with it. The third day we headed upstream to fish. Just around the bend, less than 100 feet from where we got our water, lay a dead elk in the middle of the creek. We just shrugged and looked at each other, and kept on fishing. No harmful consequences. Good immune systems? or no harmful pathogens? Don't know and don't care. With all these nice systems available today, I do use them but don't really dwell on the negative possiblities.