Quick question. As some of you may know, I've had a major aquaponics disaster, where after two years, ALL OF MY FISH died in a matter of two months. I think the cause may have been a number of factors, some of which may be metal toxicity (from a water heater), poor water quality from overstocking, and then a bunch of poor choices I made to try and fix all of it.

I have two fish left (both which look like they will survive, but they're in a hospital tank).

So I used this opportunity to completely TEAR DOWN my system and move it into a more accessible area of my yard (with more sun, 360 degree access, etc). My question though is this:

I took every bit of hydroton and rinsed it off inside of a 5 gallon bucket. It wasn't a deep scrub or anything......I simply rinsed it until the water running out of the bottom of the bucket was clear and not murky. I did that for my entire 120 gallon grow bed.

In doing so, I know that I may have destroyed the nitrifying bacteria (which I don't care at this point, I just need to start relatively fresh).....but I did keep all the worms in there (which help to break down the solids or dead plant matter). Other than that, I have 110 gallons of new water in the system and going to cycle it again.

My question though: If my fish died from a parasite of some sort, would having the system run (fishless) for a couple of weeks kill off anything in there (which may not have a host to feed on)? Or should I be safe and treat the fishless system with PraziPro and Proform C, both medications used on fish to help rid them of parasites and sickness?

My theory would be even if there isn't fish in there, running the medication in there could "kill" anything that would harm the fish once I put them back in there. So any free floating parasites could get whacked by the medicine.

My biggest fear is that I will go through all this, put my remaining two fish in the tank (with new treated water), and they still die from some "mystery" which has killed all my other fish.

So again, the question: do you think I need to medicate the EMPTY tank (which has the same grow media but 100% new water), or do you think running the system without fish for a couple of weeks will kill off any parasites since they may not have any host to feed off of (unless they attach to worms).

What do you think?