Very interesting topic. More relevant to long-term situations, but definitely worth discussing.

I've heard that certain formulations of concrete are being used to create a slightly porous matrix that will effectively filter harmful organisms out of water. This was in the context of third-world development. It seems more likely that this would work better for larger organisms -- water-borne parasites, amoebas, protozoans, etc. that cause a lot of carnage in the developing world.

I don't have a link (yet) but will look around.