You are right to be concerned about the water. Pseudomonas can grow just fine in tap water, even at the level of chlorine found in public systems. We have a reverse osmosis system for drinking water. We then boil the filtered water before we use it to clean respiratory equipment. (I'm a public-health scientist, so I've checked the research available on this topic. I've also had microbiological tests done on our filtered water, and it is free of Pseudomonas and other respiratory pathogens.)
You can get a good reverse osmosis system at Costco, but unless you're handy at installations, you may need a plumber to put it in. Alternatively, the companies that sell bottled water (Arrowhead, Culligan) will also rent reverse osmosis systems, which they will install. It is important to change the filters regularly and to disinfect the system with bleach every 6-12 months. The rental companies will change filters (though probably not as often as we need it), but aren't likely to tell you how to disinfect the system. Call the manufacturer of the system for instructions.
Something else to be aware of: the dental tubing that supplies jets of water for rinsing your mouth is often heavily contaminated with Pseudomonas. My 15-year-old son (who has CF) brings a small bottle of water with him to the dentist's to rinse with instead. Incidentally, not all bottled water is bacteria-free either. One report I've seen suggests that the carbonated versions may be cleaner.
Jordan's mom