You seem to be speaking about a theoretical water system, or one that relies on an aquifer that can be considered infinitely capacious, and which recharges from its own wastewater, but that's not the situation in which the SFPUC finds itself. It has one source and it relies on rain and snow falling in one single particular place. Therefore SFPUC has to treat its supply as limited in a way that an aquifer system that's effectively a closed loop doesn't need to worry about. SF's wastewater does not recharge its water supply in any predictable way.