Certainly. Carbon only provides chemical filtration. Addition and removal of carbon will not cause any change to your biological filtration. The bio-wheels are where you are getting your bio-filtering, and very effective filtering it is. This is why you should never remove and clean the bio-wheel. That would kill your nitrifying bacteria. Even if it turns eradically, or gets what you may think is large buildup. This is normal and will not harm filtration. Simply be sure you rinse any addition to the canister before you place it inside, as water that passes over it is carried to your biowheel and any contaminants will affect the bacteria colony.