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The way it works is by CO2's effect on the pH of a standard solution, which is viewed using an indicator. When CO2 dissolves in water, it forms carbonic acid, lowering the pH. If you start with a particular solution (4 dKH solution) that is buffered to a specific pH, the small changes in pH that dissolved CO2 creates cause fairly large changes in the color of an indicator (bromthymol blue, the blue/yellow indicator commonly sold in pH test kits.) The drop checker is set up so that CO2 in the solution and the CO2 in the aquarium are related, even though the water doesn't mix between them.

Heres a crappy drawing.

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As the amount of CO2 in the tank increases or decreases, the amount going from the tank to the checker increases or decreases, which causes the color of the checker to change. You're generally shooting for a lime green checker, if everything is set up right and you're using the standard solutions. These work well, with the caution that they are fairly slow to respond to change. A shift in CO2 concentration in the tank takes time to translate into a shift in CO2 concentration in the checker because of the roundabout path it must take to get there.

Hope this helps.
 
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