I considered including boiling but thought it would fit better in a future article about water treatment methods due to the technology and effort required. I also considered desalinization but came to the same conclusion. Thanks for drawing attention to this; boiling can reliably purify highly contaminated water.
As far as wells go, a large open shaft does make the notion of clean water a little counter-intuitive, but the groundwater is being filtered through sand and sediment below the surface and is flowing past the well rather than sitting stagnantly in it. There may be a few bugs and leaves on the surface, but the water beneath is quite clean!
RE: Trekking Tech - Basic Hydration