filter cleaning

In the last few days I've read a couple of times that cleaning the filter
with tap water kills all the good bio-bugs. Is this true of any water (say,
untreated well water), or just chlorinated water? Once and a while I give
the filter a quick rinse to get the yeech off the back, but our water is
totally untreated. If you can't rinse it off, how *do* you get the yuck off?
(I'm speaking of stuff like uneaten flake food)
thanks,
Laurie