Just setup my old JBJ nanocube and from one return pump I get tiny microbubbles. I can't figure out how to get rid of them. Will this cause any harm to fish or tank or is it just nuisance?
micro-bubbles will not harm anything in the tank they are more of an eye sore than anything else. They tend to make the tank look "cloudy"
If you just fired up the tank they may subside over time. Is the return pump that you're getting micro-bubbles from pulling air from somewhere, perhaps close to the surface?
As far as the bigger bubbles under the live rock goes it's most likely the micro-bubbles agglomerating into larger bubbles. they should float to the surface
There are 2 small return pumps that are submerged in the back of the tank. They are probably 16” below water level. I can’t figure out how they would get any air.
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