- The CO2 may accumulate in the canister filter and cause it to run dry which may lead to damage to the filter (the propeller may melt)
- The CO2 may inhibit the nitrifying bacteria in the biomedia of the filter. Some (or all, I'm not sure) of these bacteria must have access top Oxygen to function and the CO2 could lower the effectiveness of the biofilter.
That being said, 5 of 8 of my tank have the CO2 injected in the canister intake and do fine.
Niko I remember reading something a long time ago on another forum that Steve Hampton posted. He said that CO2 actually helped grow more nitrifying bacteria. They develop beter for some reason in a CO2 rich environment. I don't know how true this is maybe someone more knowledgeable in this are can comment.
CO2 has nothing to with the amount of oxygen in the water, other than it causes the plants to make more oxygen.
Ammonia and Nitrite bacteria require oxygen rich water to thrive and grow. Nitrate processing bacteria are anaerobic and will only live in the absense of oxygen. So by putting CO2 in to the intake your probably shooting yourself in the foot as far as bio-filtration goes. Though I doubt the concentration of CO2 is ever getting high enough to really affect your normal nitrifying bacteria. It is a concern but most likely nothing to worry about if that makes sense.
I would only be concerned if you have a canister that doesn't like burping out trapped air/gas. My Eheims have no problem doing this and I've been injecting CO2 into them for the last couple years without any problems at all. I think there are a lot of "theories" out there about why you shouldn't do this, but I've yet to see a practical reason not to do it if your canister isn't prone to airlocking. The water flow is enough to not create an acidic condition in the canister that is any different from the tank water, it's not a closed loop like a calcium reactor.