Backyard Aquaponics
A place to discuss aquaponics

I've lost all my fish, 47 to be exact, the water is putrid. Half of my vegetables are lost too. I want to clean up, make repairs, and get ready for spring of 2022.What can I safely use to clean up the system without harming my grow beds? I also have a sealed reservoir of 500 gal of rain water which should be unaffected that I hope to use to replenish the water needed at the startup. Thank you for any consideration and guidance sent my way. 

Hiya Gil, sorry to hear about your fish, shame.
I think that once you’ve removed what remains of the fish you can then just running your system on constant flow should clean your water up after all that’s how the nitrogen cycle rolls and from memory your system has a few years under its belt so should recover soon enough.
Time to pull up the summer crop and prepare for the winter greens anyway.
Let us know how you go.