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I got some really bad advice from a garden shop guy to put some hydrated lime in my system so the plants would get some much needed nutrients. It instantly killed the 4 gold fish I had. I'm also thinking it killed my beneficial bacteria so I could be waiting for the nitrogen cycle to get established again (3-4 weeks).
*Edit* I later found out that Hydrated lime is actually excellent for raising PH. Its strong stuff so be careful and I would just use a teaspoon if you have under 20 gal system like me and then test the PH.
Ironite - I would not recommend using ironite in aquaponics - it turned my pristine white roots into a brown grey mess. At least it didn't kill the fish. If your gonna add anything use Maxicrop Seaweed extract.
I flushed the whole system with clean water and then added hydroponics liquid nutirents (many Aquaponics pros say you don't actually need to add anything once the system is over 6 months old.) Which is what I probably should have done in the first place but I really wanted to see if I could grow stuff with just fish water.