Biocube microbubble issue

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Caper

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Hello! I have a Biocube 16 that has been cycling for a few weeks now and some occupants will be added this weekend. I developed an issue with microbubbles after I topped off the water. I must have messed up the levels. In chamber one is the heater, chamber two has the stock media rack with matrix, purigen and floss and stock pump in the third chamber. I had a small trickle waterfall between chamber one and two and chamber three was several inches lower in water level. Another forum recommended to increase the water level in the third chamber but I think that actually made things worse. Any suggestions to reduce or, preferably, eliminate the microbubbles?
 
Check for obstruction between chambers 2&3 (where the sponge usually goes). I have cleared all the rubble from there and now it seems fine.
 

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