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Hmm, I have just hooked up a DIY reactor of my own and have the same 
problem.  It feeds water in from the top via a powerhead pump.  Its a very 
low power pump so I'm thinking about getting one that is much more powerful 
to increase flow and the agitation between water and CO2 bubbles.

Is there always supposed to be a level of CO2 hanging at the top of the 
reactor, or will it always be water only if everything is right?  My first 
experiment ran about 4 bubbles per second.


 From Jerry Baker:
I have constructed a CO2 reactor out of a powerhead, a gravel vacuum
tube, some 1" bioballs, and a limewood airstone. The problem is that
after a couple hours of running so much air builds up in the reactor
that there is a 1 - 2" air layer at the top. Is this normal, and how can
I prevent this other than emptying the air every hour or two?