fish, ornamental fish, aquarium

Biological Filtration & The Nitrogen Cycle In Fish Tank Setup


Biological filtration has been the subject of more arguments and controversy than nearly any other topic in the field of aquariums. A biological filter can be as simple as the live rock in a skimmer-equipped Berlin System or the suspended gravel bed and live rock of an all-natural Jaubert Plenum System. A biological filter can also be as complex as a reverse-flow fluidized sand bed/re-aeration system. The most popular biological filters are the under gravel filter and the wet-dry filter. Many years of research have been spent by both scientists and hobbyists alike, all with the same goal – to create or discover the perfect biological filtration system.

There are many biological filtration techniques in use in modern aquariums. Regardless of which method is used, aquarium owners all want to achieve the same end result, which is to convert toxic ammonia produced by living aquatic animals and the decay of proteins, into less-harmful nitrates through the cultivation of nitrifying bacteria in the aquarium system. Some biological filtration techniques make this process several steps further, by converting those nitrates into nitrogen gasses through the cultivation of anaerobic bacteria in the aquarium. This process, called “de-nitrification,” will be discussed in a future article.

The Basic Nitrogen Cycle in The Aquarium: A simple explanation. Fish eliminate most of their waste in the form of ammonia. Ammonia is toxic to most animals, so in a brand new aquarium, the first fish introduced must be very hardy species that are known to be able to tolerate ammonia in the water. Eventually, beneficial bacteria will cultivate in the biological filter, gravel, rocks, and any other surface in the aquarium. These bacteria are aerobic, meaning they need oxygen to survive, the same as us. They are also known as “nitrifiers,” as they consume ammonia and ammonia by-products and convert them into less harmful substances that fish can tolerate. These bacteria will cultivate in far greater populations, in any area where the highest amount of oxygen exists, which is usually in a filter system that is designed to promote their growth by supplying a continuous source of oxygenated water to the bacteria. This is where the term “biological filtration” comes from.


The first species of bacteria to appear on the scene in a new aquarium are Nitrosomonas species of bacteria that “feed” on ammonia, and convert it into nitrites. Nitrites are a little less harmful than ammonia but are still rather poisonous. Eventually, usually within two to three weeks, Nitrobacter species begin to cultivate. As the Nitrosomonas populations came first, it usually takes the Nitrobacter species a long time to cultivate into a full population. Nitrobacter “feed” on nitrites and convert them into far less harmful nitrates. Many fish can tolerate relatively high levels of nitrates, but if nitrate levels get too high, fish will begin to suffer.

In nature, all of the nitrates produced by bacterial nitrification are consumed by plants, algae, other species of bacteria, and other organisms. In an aquarium as in nature, nitrates are used by plants and algae as food, and in some cases, are also converted by anaerobic bacteria into nitrogen gases. A so-called “balanced” aquarium, is one where the ratio of plants or algae to fish is balanced so that all of the nitrates produced are converted or consumed, so no nitrates exist in the water. This is very difficult to achieve in practice, as such an aquarium will have very few fish, and that is not satisfying to most aquarium hobbyists. To control the nitrate levels in an aquarium, we do water changes. That is why water changes are so important. They lower nitrate levels before they get too high and become a hazard to fish.

The nitrogen cycle is an extremely important process for starting as well as maintaining key biological functions in your tank. This allows for the proliferation of ‘beneficial bacteria’ in the aquarium and in the filter media. These microbes first convert ammonia to nitrite and then again from nitrite to nitrates. Don’t worry if you are not that chemically-inclined, as this article will explain these processes. It is essential to understand this if you want to be successful in keeping fish.

Briefly explained, here are the 3 main elements that affect the health of your tank and its inhabitants.

  • Ammonia  Harmful to all creatures. It is produced in the tank by fish waste and uneaten food.
  • Nitrite – Developed by bacteria while breaking down (oxidizing) ammonia. Although the process essentially eliminates ammonia, Nitrite is still harmful to the creatures in your tank.
  • Nitrate – This is another type of bacteria that follows in the next stage. Although not as harmful as nitrites or ammonia, nitrates can still, in large amounts, have noxious effects toward fish. However, this compound is actually beneficial to live aquarium plants, as it serves as fertilizer, but still needs to be kept in controlled levels.

Now, there are two ways to get the nitrogen cycle established, with or without fish. Most purists will tell you that starting it with fish is ill-advised. Many fish are unable to survive this beginning stage of cycling, as they are exposed to high levels of ammonia and nitrites. They may become stressed, diseased, and eventually end up dying.

There are certain species however that has proven able to endure the initial cycling. Danios or Barbs for freshwater and Damselfish for saltwater, would be good examples. Although not always guaranteed, this method is one of the quicker ways to get your tank’s nitrogen cycle going.

Ultimately, having some initial patience will result in a more stable system, and in the long run will prove better for your live stock’ health. This process may take anywhere from 1-2 weeks to 1-2 months. Here are some ways to cycle your tank without fish.

  1. Drop a small piece of raw fish or shrimp in your tank. As it decomposes, it will release ammonia – starting the cycle.
  2. Use 100% ammonia. This method requires a bit of ‘keeping track.’ Utilizing a dropper, add about 5-7 drops of ammonia per 10 gallons of water. Use a test kit to measure your ammonia levels. This process may be repeated daily or until you start to get nitrite measurements with your test kit. Once your nitrite is established, reduce the ammonia dosage by half until you get sufficient nitrite readings. After this, do a 30% water change, and your tank will be good to go.
  3. Use liquid “solutions” that have beneficial bacteria. Products like ‘Colonize’ or ‘Biospira’ are available at reputable fish stores. Or use gravel/filter media from an established tank. These methods are a little more costly, but are the quickest 
  4. For saltwater tanks, use live rock. These should be available at your local fish store. This is widely accepted as one of the best ways to establish a biological filtration system in your saltwater tank. Live rock has a “coating” of organisms that are naturally present in coral reefs.

Once the cycle has started only add one or two fish at a time. Wait a couple of weeks before adding more fish. This will give your tank the time it needs to catch up with the increased bio-load.


So what is the perfect biological filter? The perfect system would allow an aquarium owner to maintain a beautiful aquarium with plenty of desired livestock, with a minimal amount of work required to maintain the system in peak condition. We have conducted plenty of our own research on biological filtration in our aquariums and has installed various systems over the years. It is our opinion that the perfect biological filter is one that best meets the needs of the aquarium occupants. The first priority is the well-being of the fish and invertebrates we maintain. You should design aquarium filter systems around the type and quantity of animals our clients desire. Our goal is always the same: Keep the animals entrusted to our care alive and healthy!

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