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http://www.radio-media.com/fish/UnderOverUnder.jpg
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There should not be any bubbles if a scrubber is set up correctly with smooth flow into the water below. But if you have too many bubbles, make sure the bottom of the screen goes all the way down below the waterline, so there is no waterfall off the bottom, and design the scrubber with an "under over under" divider section like some people use in sumps.
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