crack in bulkhead hole

It's hard to tell from the OPs photo if it's glass or acrylic.

I personally wouldn't use silicone as a 1st resort. I've had stubborn cases where an oversized hole made it difficult for the rubber gasket to seat properly and silicone was used.

The reason why I bring up glass or acrylic is due to the adhesion properties between both materials. Silicone doesn't stick well to silicone and would require some extra steps to ensure a water tight seal as opposed to glass.

If I opted to use silicone on acrylic I would apply a thick bead around the flange of the bulkhead and set it in place only slightly tightening the nut so that the silicone filled small small gap. I'd then allow the silicone to cure before tightening. Glass on the other hand, I wouldn't be so thoughtful.

However, I'm with Troyllee on this one. I wouldn't add silicone unless absolutely necessary.

In fact I recently ran into this issue with setting up a large 550g system in where the holes drilled were just larger than necessary. The flange and seal covered the hole but the slop made it difficult to seal.

Instead of using silicone, I actually made a mold and using 2 part silicone I made thicker silicon gaskets.
 

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