It would depend on where it gets its water. Is it independent in the sense that it is buying the gallon water from the grocery store, or is it coming from the pipes under the city? If it's the former, the water in the bottles are all safe since they come from the outside. If it's the latter, all of those eventually find their way connected to the waterway.

But it is all right with us if you want to use the place as a shelter for the evacuees and other characters!

They can keep the contaminated water, but keep in mind that the strength of the diluted black blood is not very strong from the start. It would be interesting under a microscope, though!