There is a medical researcher here in California who is also a passionate backcountry enthusiast. He has access to a very high tech lab. He has, over a period of years, taken water samples from all over the Sierra Nevada. He's reached some interesting conclusions:
1. Water in the Sierra Nevada is generally safe to drink.
2. Water in the Sierra Nevada is generally cleaner than most municipal water supplies.
3. Giardia cannot survive the winter in the Sierra Nevada above 10,000' due to harsh freeze-thaw cycles.
4. Water near permanent human habitation is generally NOT safe to drink.
5. Water in areas where livestock grazing is permitted is generally NOT safe to drink.

I try to base my water treament decisions on the above. Close to trailheads or in heavily used areas, I treat my water. If there is livestock anywhere in the area, I treat the water.

On the other hand, in lesser used and remote areas, particularly above 10,000', I don't treat my water at all.

HJ