Ammonia and the nitrogen cycle in Aquariums for beginners

What is the Ammonia and Nitrogen cycle and what is this have to do with aquariums? How does it affect my fish?
Well, these are one of the many questions that every beginner aquarist has when he learns about the Nitrogen cycle which is the cause of many deaths of fish the first week in the new tank, as well as, the reason that many beginners stop the hobby.


In nature, every organic matter such as plants, dead animals, wastes, and the food is broken down by microorganisms to simpler substances. In our case, nitrifying bacteria such as Nitrosomonas and Nitrobacter brake-down the ammonia to nitrites and last to nitrates. After that plants and algae use nitrates as a source of nitrogen for protein synthesis and the combined activity of both bacteria and plants cleans the water. However, in the aquarium that is a small and closed ecosystem, the nitrates are removed by partial water changes. In the aquarium, bacteria multiply every 15-20 hours and grow mainly in the filter, as wells as, on the gravel and glass.

So if the bacteria break down the toxic substances, why is the Nitrogen cycle the most common factor for the loss of thousand fishes in a few days or weeks?
Like all living organisms, bacteria need a food source so they can grow and multiply. So, fish get infected and die in a new uncycled tank as a result of the small population of bacteria that are not able to utilize the whole ammonia. Nitrifying bacteria take several weeks to a month to sufficiently multiply in numbers and use the ammonia, a crucial fact that some people who work in pet shops ”forget” to inform their customers and especially those that are new in the hobby. In conclusion, the Nitrogen cycle needs several weeks to complete and the exact time varies by the bacteria growth.
The bacteria growth is affected by:

  1. pH: Nitrosomonas bacteria grow slowly in pH lower than 7, while Nitrobacter bacteria grow slowly at high pH.
  2. Dissolved oxygen: Nitrosomonas and Nitrobacter are gram-negative and aerobic bacteria which means they don’t convert ammonia without Oxygen. Nitrification stops if Dissolve oxygen levels drop to 2 ppm or less.
  3. Temperature: Bacteria grow faster in higher temperatures (25-30 Celsius), while in lower temperatures grow slow (18 Celsius).
  4. Salinity: Bacteria grow in a range of 0 to 6 ppt.
  5. Chlorine-Chloramine: Water with chlorine and chloramines kill the bacteria and slows the duration of Nitrification.
  6. Other factors

Ammonia (NH3) is a combination of nitrogen and hydrogen and produced by the degradation of waste products, as well as, excrete from fishes by breathing out. Furthermore, large quantities of this toxic compound are lethal to fish and just O,25 ml of ammonia in the water is enough to damage the gills and making it difficult for the fishes to breath. Some signs that may indicate that your fish suffers from ammonia toxicity are:

  1. When the fish gasps for air at the surface of the tank
  2. The fish has red or bleeding gills
  3. Increased mucus production.

Nitrites are a compound of nitrogen and oxygen that Nitrosomonas bacteria reproduced by the oxidation of the more toxic ammonia. Furthermore, a high concentration of this compound causes nerve damage, as well as, the decrease of oxygen absorption by the blood. The ideal quantity of nitrate in the water is 0-0,2 mg/l, while Concentrations above 0,5 mg/l are harmful to the fish and much higher concentrations (>1,6 mg/l) are lethal.

Nitrates are the end product of the degradation of ammonia by the Nitrobacter bacteria, which is less toxic than the other two substances. High quantities of nitrates stress the fish and weaken their immune system. Furthermore, the nitrate limit for freshwater fishes is 110 ppm and as I mentioned earlier are removed by partial water changes every week. When the Nitrogen cycle is complete, test nitrates every few months to ensure that levels are stable and safe.


In general, testing the parameters of the water is crucial for the maintenance of the tank and the health of our fish, especially when cycling a new tank. There are three types of indicators:

  1. the strip testers which some of them don’t contain ammonia tests.
  2. Most aquarists use the liquid reagent tests kits which are accurate and more reliable than strip testers.
  3. electrical meters which give specifically accurate results, but are quite expensive than the other two.
Rainbow Chemistry by Jellaluna/ is licensed under
CC BY 2.0


We learn what is the Nitrogen cycle and the nitrifying bacteria, as well as, their importance in the aquarium, so what is the next part?
There are two ways of cycling a tank:

  1. By using a small number of fishes to reproduce ammonia in the tank (fish-in cycle)
  2. Without fish, but adding ingredients to produce ammonia. (fishless-cycle)

Fish-in cycle:
When you add fish in the tank, produce ammonia with their wastes and breathing and triggers the bacteria to develop and colonize in the tank. The method’s duration is affected by the liters of the tank and the number of fishes. However, This method is not recommended by most people, as most fish will die on the prosses of cycling the tank, as the ammonia will rise. Furthermore, you need a lot of effort to keep the fish alive by:

  1. monitoring the water parameters daily with tests
  2. water changes up to 50%
  3. using Converting products for ammonia.

How to cycle :

  1. First set up your aquarium with substrate, decorations, plants and dechlorinated water. Furthermore, run the filter and the air pump continuously. Then add a few fish.
  2. Test daily the water parameters and dose every 24 hours with a product that converts ammonia to nitrates for the protection of the fishes. Usually, ammonia builds after three days from the introduction of the fishes in the tank.
  3. Start double-dosing every 24 hours when ammonia levels reach 0,5 ppm.
  4. Perform a 50% water change every time that ammonia levels reach 1 ppm.
  5. After a few weeks ammonia levels, get low while nitrite levels rise. Double dose when nitrites levels reach 0.5 ppm.
  6. Perform a 50% water change every time that Nitrites levels reach 1 ppm.
  7. If thing goes right, ammonia and nitrites levels will get lower while nitrate levels will get high. When nitrate levels reach 30 ppm, perform a 50% water change.
  8. The cycle is complete when the ammonia and nitrate levels reach 0 ppm.
Freshwater aquarium is licensed under
CC BY-SA 4.0

Fishless cycle:
This method is less dangerous from the fish-in method as there are no fish. In this case, a source of ammonia such as fish food, aquarium products or 9,5% household ammonia is used to start the cycle. Add a small amount of fish food every day and remove the old food before it starts to rot. Using the method with fish food is challenging to control the released ammonia levels while using household ammonia is easier which you can purchase it cheaply in DIY stores. Be extra careful if you choose to use pure ammonia as a source to cycle your tank. Don’t use ammonia solution with ingredients other than ammonia/ammonium, hydroxide, and water.

How to cycle:

  1. First set up your aquarium with substrate, decorations, plants and dechlorinated water. Furthermore, run the filter and the air pump continuously.
  2. Add a source of ammonia to start the cycle such as fish food, aquarium products or 9,5% household ammonia. Add 1ml per 25 liters of water until ammonia levels reach 4ppm.
  3. Measure the water parameters daily for ammonia, nitrites, and nitrates. Add ammonia every time that the ammonia levels drop to maintain the ammonia levels to 4ppm. It’s normal for the water to get cloudy from the increase of bacteria’s population. The water will clear in time. After a few days, you may add exogenous bacteria to speed up the process.
  4. After 1-2 weeks, nitrite levels start to rise while ammonia levels drop. So, to ensure that you are supplying the bacteria cycle, keep adding ammonia. Test nitrites one hour after adding ammonia.
  5. When ammonia and nitrites levels drop to 0ppm, then stop adding ammonia. As nitrates will never reach 0ppm, control them up to 40 ppm or less by partial water changes every week. Furthermore, aquatic plants help to reduce the nitrate levels by using them for protein synthesis.


  1. An introduction to fishless cycling. Retrieved from:
  2. Dr. Richmond Loh, Ammonia Nitrite Nitrate. Retrieved from:
  3. Step by Step Guide to Fishless Cycling. Retrieved from:
  4. Introduction To The Nitrogen Cycle. Retrieved from:
  5. Thomas Reich 2018, Nitrogen Cycle in Aquariums. Retrieved from:

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