Gradual decontamination: good idea or bad?

[Ben Stallings]

I was feeling really psyched about my first aquaponic setup, which you can see in this brief video: https://www.youtube.com/watch?v=R-QSVILv9gI .  I gave a presentation to a local school group and got them all excited.  Then most of my goldfish died.  I'm down to 3, from 10.  They all hunkered down at the bottom of the tank and remained motionless as possible, then floated up as they died.  I've done some reading on this sitting-on-the-bottom behavior and there are lots of potential causes, so I have to start with the most likely...

I'm pretty sure the problem is that I started adding rainwater instead of dechlorinated tap water, and the rainwater I have access to is collected from my roof, which has asphalt shingles that were replaced less than 6 months ago.  So although the plants are happy and all the chemical tests are in normal ranges, I think I have some "toxic gik" (as Paul Wheaton would say) in the system.  No oil is visible on the surface of the water, incidentally.

I know the standard solution (no pun intended) to this problem would be to pour out all the water and start fresh, but I'm reluctant to do that because the plants seem to be cool with the current water, which is loaded with nutrients.  I guess I could lug all the water upstairs to my outdoor garden, but we're about to get a ton of rain, so I have another option in mind, which is to keep the system working while gradually decontaminating it with clean water.  Here's my idea:

1. Put the remaining fish in a spare, non-plumbed aquarium with known clean water: dechlorinated tap water and/or condensate from the dehumidifier.  Maybe add a few rocks from the grow bed for biofiltration.
2. Twice a day, at feeding time, remove a half gallon or so of fishy water and waste from the spare aquarium, replacing it with an equivalent amount of known clean water.
3. Just after doing that, remove an equivalent amount of presumed-contaminated water from the aquaponic system (which no longer has fish in it) and replace it with the fishy water.
4. Pour the presumed-contaminated water on outdoor plants.  Fill the empty container with tap water for dechlorination.
5. After a week or so of doing this, buy some new fish and see if they survive in the aquaponic system.

My question for you is, is this more trouble than it's worth?  Would I be better off just changing all the water at once?  Thanks for your feedback!

[Ben Stallings]

Yes, the goldfish were cheap, so disease is one of the many other possibilities.  A couple died right away from shock, but the rest lived for about 6 weeks in the system.  The aquarium had cycled with bottled ammonia for about 2 weeks before I introduced the fish.  The three remaining fish were still alive as of this morning.

Randall, thanks for the recommendation, but I'm not sure what you're suggesting.  Are you saying to leave the fish in the system and replace 20% of the water while they're in there?  My thinking in removing them from the system to an external tank was to eliminate any new exposure to whatever the toxin is, until it's diluted enough to no longer be a problem.

[Ben Stallings]

Well, my plan backfired, as the fish I moved to the clean tank died before the one I left in the system.  I expect he's not long for this world either.  I'm going to go ahead with changing out some of the water, and I'll keep the system going with bottled ammonia for a week or so before I buy more fish -- fewer and better quality.  Thanks for the advice!