I used to speculate it was evolutionary.
You piss in the water because it helps cover your trail (so predators can't track you).
You don't piss in the waterhole, especially if you plan to stay there for awhile, its unhygienic. On the other hand, its OK to take a leak in a stream, because the current will disperse the scent. But I really don't know.
Its one of those mysteries from our deep past; like, why are yawns contagious? Or why are farts funny?