I've seen questions like this in other contexts, especially with projects wanting to get a green certification reflecting what takes place in the building, not just the design of the building itself. Factories, for example.
I would say that LEED is set up to certify, most classically, an office building. This can be extended to admin buildings, even wastewater treatment facilities, but the LEED certification will tend to have less to do with the main thing of what goes on in the building (wastewater treatment) and more about how it is built and operated.
It would be cool to see separate guidelines for this type of project, but I am guessing it would take a move on the part of the wastewater treatment industry, or municipalities who own and run such facilities, to make this come together. It would take some expressed demand to make it happen in LEED, as far as I can guess.