I have been battling health issues(ich,fungus)in my tank for months. Water quality is mostly to blame. Ammonia is hard to control unless I change water every 2 days. Tank is 8 months old and not over populated or overfed per advise from OFL over the last month. I am upgrading my filter to an fx5 in 120 gal tank. My question is can I do this while treating my tank with meds? I have been trying to wait but I cant seem to get tank healthy with my current system(I will transfer bio material and cotinue to run old filter until new filters bio catches up.

What meds are in the tank? please tell use all that have been used in the last month. also there is no point moving media and running both filters. cos either way one would end up with no media, it would be best to wash out the dirty media in the tank so the fx5 takes in the dirt. then assemble the old filter and continue to run for 6 wks. all this will depend on the meds you are using of cause.

I would also recommend a product called cycle

They are both products by Kordon. 1 is Ich Rid which is meth. green based and the other is Fungus rid which has several kinds of herbs. After listening to OFL I know that I am hurting my bio by treating with these meds,however will getting better filtration and continued treatment with meds help my problem. I also do plan on usind old bio in new filter like you said.

the problem is the media in the filter contains good bacteria, once you add meds that kill that bacteria it will take up to 6wks to recover. by adding another filter this to will need 6wks to build its bacteria. so in one way adding another filter to your tank is necessary but is a waste of time until the meds are finished there job of killing all the infection.

what you need to do is change water to keep the water conditions good and add medication to the new water to replace whats removed by the water change.

once your fish are healthy then add the new filter and cycle. I wouldn't bother moving the media from the old filter cos it sounds like it is damaged already. i know its a pain to keep doing water changes but its the only way to keep good condition. without good conditions the meds won't work.

once your fish have no infection do a 30% water change.add your new filter with just carbon inside and run for a wk during this wk do some smaller water changes if you can. this is to remove all medication. after the wk open the new filter remove the carbon and fill with your media.add cycle to the tank then run for 6wks. watching your water condition for ammonia/nitrites and doing water changes when needed.

Marcus has you covered

Thank you. My new filter is an fx5. Will it be enough if I fill a couple of big media bags with carbon and put in the first basket? I dont need to fill all 3 baskets with carbon, do I?

A couple of bags should do it

In the future what do you think of a hospital tank? If I set one up do I need to keep a few feeder goldfish in it to keep the bio active once it is cycled?

all you need for a hospital tank is of course a tank and a seeded filter.
i keep a small hob running on my main tank just for that purpose. if i have to put a fish in the hospital tank i just fill it with tankwater and transfer the hob to it and presto instantly cycled tank.

So do you even have water in the tank when no one is sick.