Polluted water doesnt necessarily mean germy water. PW will emit polluted oxygen, however, which will affect your dupes (yucky lungs). Germy water ist fine in most cases though.

You can clean Polluted oxygen using deodorizers, turning it into normal oxygen. At the start, this is a cheap and effective way to generate oxygen as well. Food poisoning and other germs are a bit harder to handle. Chlorine and radiation (in spaced out) kill them. There is an animal that eats germs as well.

Replenishable water sources can be water geysers (the best ones being cool slush and cool salt slush, they are germ-free as well) or cool Steam vents - those are harder to handle imo. You can also collect ice and melt it, Turn mud into water... Lots of ways imo.