Carbon use in the aquarium seems to be misunderstood. It seems like almost every book recommends it. Most aquarists use it. Every filter has it either built in or available as a separate media. However, it is completely unnecessary for constant use.
Carbon has certain functions in the aquarium. The main one is removing medications. Many medications are very strong and harmful and if not used properly or left in the tank too long can end up causing more harm than good. Because of this it is a good idea to use carbon to remove medications after treatment is complete.
There are a few other benefits of carbon. They are mainly in the removal of odor and discoloration. However, these things should not be an issue at all if enough water changes are being done. At this point it would simply be ‘if it can help, why not use it?’ That is where the other issues come in.
Carbon is not selective. It removes a lot of different chemicals whether they are good or bad. Some of these are trace elements and micronutrients. These are vital for the proper physiological function of fish, plants, and invertebrates. When these nutrients are removed it can lead to many physiological dysfunctions in the organisms. One possible result in some species is Head and Lateral Erosion (HLLE). HLLE may or may not include erosion of the lateral line. Generally the symptoms are shallow, wide pits on the head, sometimes also on the lateral line. As the condition progresses it can cause the loss of a lot of tissue and can result in the death of the fish.
I believe that many other species have other problems that are simply not as easily observable as HLLE. What we see as a three year old tetra dying of ‘old age’, some recent change in the tank, or simply unknown causes may actually be the result of a physiological dysfunction caused by a poor diet and/or nutrients being removed by carbon. If the carbon removes these nutrients then the fish can’t use them. This can lead to these unseen internal problems. Since almost no fish have necropsies performed there is no way of knowing if this is true or, what I believe is more likely, how bad the problem is. We know from human health that most problems are subtle and internal. The fish cannot tell us that anything is wrong and we cannot detect almost any problems until there are obvious external symptoms. This limits us to relatively few problems being detectable.
There have been cases of HLLE where the only change needed was the removal of carbon. In these cases the HLLE developed while carbon was being used. Sometimes other treatments were attempted and either had no effect or did not fully solve the problem. When the carbon was removed the HLLE went away. In some cases the carbon was returned and immediately following the return of the carbon the HLLE returned as well.
As if this wasn’t enough, most carbon is not effective after a certain period of time. The quality of the carbon is a major factor in how long the carbon will be effective. In addition, the amount of chemicals in the water that will be removed will also affect the lifespan of carbon. In general high quality carbon will last from two to four weeks. Most people do not change their carbon frequently enough, so for at least part of the time it is in the filter it is not providing any benefit anyways.
In most aquariums a healthy water change schedule will prevent any problems associated with not using carbon. Using carbon to prevent things like discoloration or odor is simplyhiding a symptom of the real problem of inadequate water changes.
The debate about whether carbon really is harmful or not is caused by the fact that carbon removes things like trace elements. Most tanks are not so well balanced that trace elements are their limiting factor. In most cases there are other, bigger issues that are holding things back. For example, in a planted tank the lighting, carbon dioxide, etc. is more likely to be a limiting factor. In a reef tank lighting, calcium, alkalinity, magnesium, food, etc. are all more likely to limit the corals than trace elements. But in tanks that are well balanced enough for trace elements to be the limiting factor people have seen their plants or corals do better when they stopped using carbon. Others who have done the same and not seen a difference have not proven that carbon is not an issue, but simply proven that their tanks weren’t perfectly balanced.
In order to balanced the benefits of the bad things that carbon does remove with the consequences of the removal of the good things, many people will run carbon for only short periods of time on a regular basis, like 24 hours once per month.
In summary carbon is an unnecessary and even harmful media that does not need to be used in the aquarium except for short-term applications such as removing medications. When choosing a filter pick one with customizable media that does not require you to use carbon. Avoid those that provide combined cartridges that include carbon built in to mechanical media. When using customizable filters use more biological media in place of the carbon.