Filtration is the process that allows us to keep fish alive and healthy outside their natural habitat.  It helps clean the water so that the fish can live for extended periods of time without constant aquarium maintenance. Waste products excreted by animals which include ammonia are extremely stressful and life threatening. The primary purpose of filtration is to remove toxic waste products produced by aquarium animals. They work by using a combination of three types of filtration:

Mechanical

Mechanical filtration is the removal of particulates floating in the water column. Generally, this is the first stage of filtration, and is a physical process acting like a sieve as water passes through a medium that selectively traps large particles out of the current.  This can help keep the water from being cloudy or silty and make it crystal clear.  The medium used can be substrate (such as gravel or rock), sponge, filter cotton floss, a micron sock or diatomaceous earth powder. Mechanical filters will clog over a time period and will need to be cleaned or replaced when this happens.

Chemical

Chemical filtration generally follows mechanical filtration in most filters.  A chemical filter is a medium that chemically traps or releases compounds as the water passes over and through it.  There are many chemical filters that can be used to freshen water, but carbon or charcoal is the most common.  Carbon is a substance that has many pockets and bonding sites on it, so that impurities, colors, and odors can attach to it, much like a magnet.  There is a finite amount of these bonding sites, so eventually the carbon must be replaced.  Some chemical mediums (i.e. resins) work like a “sponge” and absorb certain elements and ions from the water. It is important to note that while carbon can help “clean” a tank from byproducts and pollution, it is not a suitable replacement for biological filtration.

Biological

This type of filtration is by far the most important for keeping fish in an aquarium.  From the moment fish are introduced into the aquarium, they begin releasing ammonia, their principle waste product.  If allowed to build, this ammonia can kill fish by damaging the gill tissues and preventing them from taking in oxygen.  Beneficial (good) bacteria help us filter the water through a biochemical process.  Essentially, waste laden water passes over bacteria, which consume the waste and convert it into less toxic compounds.

Nitrosomonas bacteria are traditionally held as the bacteria that are responsible for converting ammonia into compounds called nitrites. The establishment of a healthy reproducing colony of these bacteria takes about 2-3 weeks.  These good beneficial bacteria are known as aerobic bacteria (or oxygen loving). This means that this particular type of bacteria needs oxygen in order to live and function. Giving the bacteria a surface area (such as filter media of any type, decorative gravel substrate, etc.) along with oxygenated water will allow for explosive growth of a bacterial population. Once created in the filter media, these bacteria will instantly convert all ammonia present in the water into nitrites.

Nitrites, though, are fairly hazardous compounds to fish health as well, so the filter must employ the use of another group of aerobic bacteria to adequately filter the water.  Nitrobacter or Nitrospira bacteria are held accountable for the conversion of nitrites to nitrates.  These bacteria behave in a similar fashion to the Nitrosomonas bacteria in that they will consume nitrites and release nitrates as a waste product. Two weeks are generally necessary for these bacteria to fully seat themselves into a filter’s media.  Again, once established, these bacteria will instantly convert all nitrites present into nitrates.

The growth and establishment stages of bacterial colonies are what are referred to as “cycling” the aquarium. In all, it takes 4-6 weeks for the cycling to complete.  However, once complete, the bacterial colonies will continue to reproduce on their own, sustaining themselves on fish waste and organic material.

The initial explosive growth of these bacteria, cause what is referred to as a bacterial bloom. There are so many reproducing in the water column; they will make the water look hazy or cloudy. Do not be alarmed, nothing is wrong as this is a normal process needed to “kick start” the development of these “good” bacteria. Once enough have grown and filled the filter media the rest will die off and the aquarium water will get crystal clear. This usually takes a few days.

To clean a biological filter, it is critical to remember that the media involved house billions of living bacteria, and that the absence of these bacteria can result in the loss of all other living organisms in the aquarium. Usually, the media responsible for containing the bacteria are positioned last in the flow of a filter or are constructed of flow-through materials, so that they collect the least amount of physical waste. When it is necessary to clean it, usage of old aquarium water (left over from a “water change”) to rinse the media is essential. Never use chlorinated tap water as the chlorine will kill the beneficial bacteria. Ideally, the rest of the tank is left untouched when cleaning biological media, for it too houses bacteria, and they will help pick up the slack when the main component of bacteria are under stress from cleaning.