http://en.wikipedia.org/wiki/Great_Lakes_Compact
There are rules governing what a waste water treatment plant can output (especially around things like phosphorus). On a river, one town's waste water is the next town's source water.
New York City owns large tracts of land to help protect its water supply:
http://en.wikipedia.org/wiki/New_York_City_water_supply_syst...
http://www.pwconserve.org/issues/watersheds/newyorkcity/
There are also usually pretty strict laws in force anywhere surface water is used for drinking water (you see watershed signs for that).
Of course new and changing interests will require lots of changes to the way the oversight it done, and it anyway isn't exactly perfect.
If you don't water you lawn, you're fined. If you do, you're fined.
And here's an example of a guy going to jail for having a rainwater pool on their property:
http://www.realfarmacy.com/oregon-man-sent-to-jail-for-catch...
And a state law trumps a Homeowner's Association (it's normally even written into the contract). The Association is liable for attempting to enforce something that violates state law.
> And here's an example of a guy going to jail for having a rainwater pool on their property
Um, IIRC, the details of that case are that the dude actually build enormous reservoirs. We're not talking a couple barrels, we're talking something like 3 ponds.