BCOrchid,
A few things that I can see won't work with your idea.
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just have a bucket with some aragonite and a bit of CO2 bubbling away in there...
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With an open topped bucket all you are going to do is send the CO2 bubbling back into the atmosphere. The reason Ca reactors are closed loops and are sealed from the atmosphere is so that the CO2 doesn't come out of solution and lose it's effectiveness at lowering the pH of the effluent. When running a reactor one of the ways to remove CO2 from the effluent when you are returning it into the tank is to allow it to sit in the open air so the CO2 is released prior to entering the tank. To get any noticeable effect by doing what you are saying you'd need to run a massive CO2 system as the bubbles will just go to the surface and pop.
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I figure if it went into my sump then through my pumps etc and then through the water fall back into my tank that should rid the water of excess CO2.... shouldn't it?
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You wouldn't have to worry about that as there will be very little CO2 in solution. There is nothing forcing the CO2 into solution. By sealing the reactor and chopping the bubbles up very fine you are giving the water in the reactor a much larger surface volume to interact with the CO2.
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but having it run through my freshwater auto top off
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You are going to want to run it from your tank itself. Most reactors run at about 100ml/min or more depending on tank demands. I highly doubt you are putting that much fresh water into your system for top off. As well I am not positive but using fresh water won't have the same effect in a reactor. I can't say how the whole chemical process will go. but. I'd say no go.
How a Ca reactor works is that it takes a volume of water inside a sealed chamber mixed with media and recirculates that water. Forcing the water to be in constant contact with the media. You then insert CO2 which takes the pH down to a low enough level to break the media down. you then introduce water from the tank and this forces effluent out of the reactor into your tank. in a nutshell that it it.