you could remove the carbon, or just wait a day or two after putting in new carbon then fertilize. carbon is only effective in removing things for a short while. after a day or two, it has absorbed all the bad things it can, and can not absorb more, be it toxins, or fertilizers. so, if you wait a day or two, just fertilize, as the carbon wont be able to absorb it. i myself am a carbon user, but honestly for normal day to day use, it doesnt do a whole lot for you, other than cost money. it is great for removing meds, and toxins from an aquarium after you have treated it. but for daily use, you are better off putting in a chunk of porus sponge in your filter that will grow beneficial bacteria on it.