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I've used apple cider vinegar a couple of times to clean my filter for my 10 gallon nano. I've always made sure to rinse off everything really well a few times before adding back to the tank though. That would be my advice. Just make sure you rinse off all the vinegar and wipe down the parts good and you should be absolutely fine.
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10g mixed reef and 20g long office reef build
"Greatness is not in where we stand, but in the direction we are moving. We must sail sometimes with the wind and sometimes against it - but sail we must and not drift, nor lie at anchor."
- Oliver Wendell Holmes
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