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I have pond filters (black, coarse foam) inside my filter socks to quiet the water splash noise. I haven't noticed any problems. Not sure if this is what you are referring to.
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I would recommend the emaco cement. I install ponds and work with pond foam on a regular basis. We do not use the great stuff foam, we use the aquascape pond foam. I'm not sure if they are different or not. The foam I use holds up very well in ponds, however I do not have any experience using it in a reef tank. I am pretty confident that it would work, but not sure if it would last as long in saltwater. The aquascape pond foam claims to hold up for 30 yrs in a pond. If to are going to go the foam route I would suggest doing a little practicing with it first as there is a bit of a learning curve to using it. By practicing you will get the feel for how much it expands and how much you will need in the "gaps". When we use it in ponds we usually wait until it starts to get a little tacky and put pea gravel on it to disguise it so that you do not see the black foam. You could most likely break up some dry or live rock and do the same so that the black doesn't stick out as much.
I have heard several horror stories about the yellow great stuff foam. It degrades quickly in saltwater. I would rather trust something that I know is meant to see water.
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Also when you're using it wear gloves it will stay on your skin for weeks.
+100!! dang. cant believe I forgot to mention this!! WEAR GLOVES! i do a lot of work without them, because thats just how I do. But, I wish I wouldve worn gloves with the black foam!! Weeks is no exaggeration.
Lol yea man it's nasty stuff. The only way I have found to get it off is to literally file it off with a pumice stone. I hate wearing gloves, the only time you will see gloves on my hands I'd when I'm using the foam.

