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Troynel, we're going to need a little more info to give an answer specific to your setup, but the reactor gives the CO2 a place/method to dissolve into the water. Are you using a sump or canister setup?
 

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You can certainly plumb the return line of the reactor into the sump pickup, that's what I do. Running the CO2 supply line into the sump pickup will not result in sufficient absorption of CO2 into the water, that's what the reactor is for.
 

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Usually the reactors have bioballs or some other media to trap the bubbles so that the water has a longer contact time with the CO2. The air gets trapped by the balls and small amounts are dissolved into the water little at a time.
 
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