How to seal interior aquaponic system?
Aquarium grade Room Temperature Vulcanizing (rtv) silicone will not harm fish life - it's what holds nearly every glass aquarium made in the last 40 years or so together. If the aqaurium in your picture is glass, it's probably glued with silicone. Read the label on the tube. Somewhere in the fine print there will, or will not be a mention of suitable for aquarium use. If it's not there, don't use it. If it is, use it, paying attention to required cure times. Honestly, the PVC is more questionable than silicone; look up organotins.

Unless you really want to pay extra, the product will be sold as clear silicone caulk (it may or may not actually say RTV, but it is) and you just need to find the fine print in question on it.

Of course, if it's remotely like the picture you can also just  poke a hole in the SIDE of the pot at the proper level - anything "leaking" from there will "leak" into the aquarium.