Giardia, the most common diarrhea-producing organism in the wilderness originates in small animals and birds. You can't get upstream from them. Also, water gurgling from a spring may be flowing into the ground from a polluted area on the other side of the hill. And chemicals from agricultural and industrial runoffs are an increasing problem in most parts of the world and have become an important source of GI illnesses. These containers often have narrow openings making them difficult to clean, sometimes resulting in the containers becoming sources of infection.
Disposable bottles are better.
In developing countries suspect locally bottled water. The water is only as good as the product that goes in the bottle. When there is doubt, choose international brands or carbonated water. Carbonation acidifies water and destroys organisms. Inadvertently swallowing water while swimming or engaging in water sports is another important cause of GI diseases.