I mean, you could have hit the germ overlay...
A big thing you can do, is create a closed loop for the toilets, sinks, showers.
Showers, sinks and toilets do not care if the water is germ free. And showers and sinks are 1:1 intake/outtake of water/polluted water.
Toilets actually CREATE water. (technically not create, that magic water comes from dupes poop/urine, which comes from dupes consuming food, which needed water to create.)
But, the point is, you can loop them, and never run out of water. and in fact, it fills up, and you have to dump water out of the loop periodically.
The, yes, you can run these pipes through cholorine and it will cleanse the water/polluted water of germs even in the pipes. A liquid reservoir is even better, due to the excess water mentioned.
oxidizers dont care about water temp, or germs. (short of boiling/damaging water) they output set temp, and kill germs.
Irrigation does not care about germs either.
Cooking, cares about germs.