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How high is the water level in your tank? I usually only see tiny bubbles in the tank when the output from the filter 'falls' onto the water surface when the water level in the tank is low.
 

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@Riptide Micro bubbles are normally in the water column but if you are seeing small bubbles on the water surface it may be due to something else.

How are you cycling the tank? Are you using ammonia, bacteria in a bottle or something else?
 

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Any chance you can post a pic or video of the tank with the micro bubbles?

Are the Penguin 350 filters new or used? Did you try to remove the bio-wheels temporarily to see if the micro bubbles go away?
 
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