One should note that the nice thing about fresh water is that it is - in principle - a renewable resource. Only when we are talking about ancient aquifers could we talk about something like depletion. However the capabilities of reaching such aquifers and depleting them seems to me a purely modern one. Sure, water can be used up in the sense that there is nothing left to flow into the sea. And indeed, historical societies have had (and countries still have) water shortages, but due to the renewability of it, these have always been limited events. So whole cultures collapsing due to overuse seems unlikely to me.

However the way water flows and is retained by the land is largely dependent on how the land is handled. Cutting down forests in hilly terrain may lead to erosion to bed rock and as a consequence less water retention, the same goes for overgrazing. Salinization is related to an excess of open air irrigation can have similarly negative consequences. Now this could be quantified as depletion of land resources of course, but it is heavily tied in with water use.

Many societies have and are affected by the adverse affects of bad land use practices. Whether whole societies have collapsed due to them? Perhaps someone else can chime in. For one, I know Jared Diamond (yes, I know he is despised here) has this nice theory about the decline of the Fertile Crescent and it successive civilizations, see here.