As muymalestado says - in the mountains, most people just dip and drink. The water in the west can be quite brown which is due to peat staining. Peat is sterile and makes the water very acid.
However, it might cause stomach upsets to people not used to this water - the sort of thing anybody gets whilst travelling abroad and, there is a chance that an individual might catch a nasty bug - so Mairi's advice to boil it is good. There's no need to carry water because its very freely available. Some people do filter it - and there's a thread on this forum about steripens.
Most backpackers do what muymalestado says, though, including me.
I suspect that many of us dont get ill because we're used to the water and have rather vicious personal defence systems.
In lowland areas, specially where there are cattle and other stock, I'd be a lot less trusting of wild water.
Its also suspect when its in spate due to organisms being washed into burns from surrounding soil - which is always full of c**p