If you put tap water into a sealed water bottle (or barrel), how long will it keep for? It can't evaporate there, either.

I don't really know the answer. Many people seem to think you need to add additional purifiers and then cycle water every 6 months anyway. I'm not sure that's right, but if it is, then the water in the proposed tanks wouldn't have additional purifiers, and could basically sit their indefinitely. Maybe if the water comes in at the top and leaves at the bottom, it would guarantee enough circulation that the fresh chlorides in the incoming water would diffuse through the entire system. It's just something to be thought about, rather than an insurmountable obstacle.

Bugs get everywhere. Often treatments don't so much kill them completely as reduce their numbers to what the human immune system can deal with. So a few remain and given time, they can grow back.

If you think the bugs are coming in from upstream.

I'm not sure filtering worth having can be fast enough for the through-put needed (and I've avoided domestic filters as just another place for bugs to grow). Ultra-violet light treatment could be more practical.