You might also want to ask the anthropologists over in our sibling subreddits /r/AskAnthropology and /r/AskSocialScience.

Well I don't know about Prehistoric water drinking, but here is an article about medieval water: http://leslefts.blogspot.com.au/2013/11/the-great-medieval-water-myth.html

Basically according to this, people drank water as long as it was clear and didn't smell. Now the article doesn't have anything to do with the Prehistoric era, however it shows some of the criteria they might have used when deciding whether to drink from a certain water source.