Medicate tank without harming your beneficial bacteria in your bio filter

[crunch7]

Could anyone suggest how to medicate tank without harming your beneficial bacteria in your bio filter. I think my 60 gal tank has been infected by worms , gill flukes and anchor worms and I want to treat the entire tank with potassium permanganate. They say that the bio filter should not dry up or all the bacteria will die so do I need to keep it running in an alternate bucket with some aquarium water ?

 

[eaglesaquarium]

Beneficial bacteria aren't affected by all medications. Generally just the ones that kill gram negative bacteria.

What you are describing is an infection of external parasites, primarily. Medications for external parasites aren't going to affect your biofilter. But, I would suggest some 'salt baths' for your fish to help your fish deal with the parasites a little better.

A salt bath, with a bit of methylene blue added will benefit their ability to get oxygen into their blood.

http://www.aquarium-pond-answers.com/2009/07/fish-baths.html
This link will help a lot.