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The Nitrogen Cycle and Conditioning Period in New Aquariums


A thorough understanding of how water quality affects animal life is essential if one is to be a successful aquarist.  This is sometimes a bit difficult for beginners to accept, but please remember that it is a serious mistake to spend time learning about the habits and dietary needs of aquatic creatures while ignoring the “less glamorous” aspects of the hobby.  Once you understand water chemistry basics, your appreciation of how fishes and invertebrates survive in their environments will be heightened. 


The Nitrogen Cycle

The nitrogen cycle is a critical factor in the establishment of a crystal clear, well-balanced aquarium.  Poor functioning of the nitrogen cycle is undoubtedly the most common reason behind new aquarium failures.


Basically, the nitrogen cycle is a process by which nitrogen is converted to other organic compounds that are then utilized by plants and animals as food.  Nitrogen enters the aquarium via dead animals and plants, uneaten food, and the waste products of fish and invertebrates.  The most toxic nitrogenous compound that is added to aquariums in this manner is ammonia.  Ammonia occurs in two forms, ionized and un-ionized, with the un-ionized type being extremely toxic to aquatic organisms.  The proportion of the total ammonia that is un-ionized rises as the water’s temperature and alkalinity increases.


Bacteria and the Nitrogen Cycle

Two types of bacteria control the functioning of the nitrogen cycle.  These bacteria are aerobic, which means that they require oxygen in order to survive.  Bacteria populations develop and thrive on substrates that are exposed to oxygenated water, such as gravel and the filter pads and carbon within filters.


The process by which aerobic bacteria convert ammonia to less harmful compounds occurs in two phases. Nitrosomas bacteria convert ammonia to compounds known as nitrites. Nitrites, while dangerous to aquatic organisms, are less toxic than is ammonia.  In the second stage of the process, bacteria of the genus Nitrobacter utilize these nitrites as food, and in doing so convert the nitrites to nitrates.  Nitrates are the end product of the nitrogen cycle, and are the least toxic of the compounds involved.


Nitrogenous bacteria (the name given to the various species of bacteria that feed upon ammonia-based compounds) exist in huge populations in natural water bodies and in healthy aquariums.  Until such are established in your aquarium, its levels of nitrogen-based compounds will be toxic to nearly all fishes and invertebrates.


The time it takes for healthy populations of nitrogenous bacteria to become established in an aquarium is often referred to as the “conditioning period”. Its actual timetable varies greatly depending upon the unique characteristics of each aquarium and of the animals therein, but usually falls in the range of 1-6 weeks.


Please bear in mind that water clarity is not an indicator of the functioning of the nitrogen cycle.  The only sure way to monitor the cycle is via frequent testing of the water to determine the levels of ammonia, nitrates, and nitrites (please see below).


Altering the Nitrogen Cycle

Your aquarium’s conditioning period may be shortened by the addition live aerobic bacteria.  I have had good experience with Biozyme Freshwater and Biozyme Saltwater, and strongly urge you to use either with all new aquariums.  Products such as Coral Vital LSB Pro, which accelerates the growth and reproduction of bacteria in marine aquariums, should also be considered.


You can also help the process along by adding filter material from a well- conditioned, parasite-free tank into the filter of your new aquarium.  Natural materials such as “live rock and “live sand” also host beneficial bacteria and offer another option.


In the past, it was standard practice to use hardy fish, such as domino damselfish in marine aquariums or guppies in freshwater aquariums, to hasten the conditioning period (their waste products started the process and provided food for bacteria).  However, additives such as those mentioned above are more effective and infinitely kinder, as many of the fish subjected to this process did not survive.


When cleaning your filters, always retain a bit of old filter medium (carbon, floss) and add this to the clean filtering material.  In this way, you will introduce aerobic bacteria into the newly-cleaned filter.  These will reproduce rapidly and greatly increase filtration effectiveness.


Please be aware that the addition of packaged bacteria does not eliminate the need for a proper conditioning period. Water quality must still be monitored carefully, and animals should be introduced to the aquarium in small numbers. 


Measuring the Levels of Nitrogenous Compounds

The frequent use of test kits is essential during the aquarium’s conditioning period, and on a regular basis thereafter.


Ammonia should be tested daily until you notice a sudden decrease in its level.  This decrease signals the presence of Nitrosomas bacteria.  Nitrate levels will then follow the same pattern, as the Nitrobacter bacteria become established.


The conditioning period may be considered at an end once the nitrate levels drop substantially.  You may now begin to introduce fish and invertebrates into their new home.  Be sure to add animals in small quantities, so as not to overwhelm the nitrifying potential of the bacteria present, and observe them carefully for signs of stress.


The pH level should be checked often as well, since the water may become acidic during the conditioning period.


I am very interested to hear about your successes and challenges in establishing new aquariums, and will be sure to pass along your information to my readers in future articles.  Thanks, until next time, Frank.


An interesting technical article on the role of nitrogenous bacteria in natural marine habitats is posted at:



  1. avatar

    I set a saltwater tank up 8 days ago ( only a 12gallon) I have added 5lbs of live rock the day after the ammonia level increase very slightly and than dropped to 0 the next day. I tested the levels every day and the ammonia/nitrite/nitrate levels were all 0 until 3 days later when the nitrate level rose to about 2.5 the next day the nitrate rose to 5 and all other levels were at 0 and today the nitrate is at 10 and the ammonia is at 1 I don’t know if I’m cycling or what and what I should do. Do I need to change the water or what. . Thank you.

  2. avatar

    No need to panic, the conditions that you are seeing in your aquarium are normal for a newly set-up saltwater aquarium, especially one with new live rock. Your tank and Live Rock are going through a curing and cycling process. Here is a helpful video that we have for more information about curing Live Rock.


    The Video shows the liverock being cured in a rubbermaid type container, you can perform the same process in your aquarium.

    As the rock cures you will see elevated levels of Ammonia and Nitrite,from decomposing plant, animal, and organic material on the liverock. As the beneficial bacteria in your filter,and on the liverock grows in volume, your system will start to stabilize, and eventually you should have zero ammonia and nitrite, this is when your aquarium is completely cycled. The cycling process typically takes 4 to 6 weeks to complete, so at 8 days you are just getting started. The Nitrate levels in your aquarium will slowly increase over time, performing regular water changes with quality water and salt mix will keep your nitrate levels under control.

    Hope this helps,


  3. avatar

    Hello How i can post images here ?
    I try upload it, but something wrong.

  4. avatar

    The comment field does not allow for uploaded or referenced images to be visible. If you would like to use an image in your comment, I’d suggest just linking to it.

  5. avatar

    I have a 55 gallon tank 5 weeks old with two barbs. The ammonia is going through the roof it is 4 ppm It is going through the cycle. Is this normal. Should I be cleaning the tank the gravel etc… I was under the understanding that i should let nature take its course for 6 weeks. I am also starting to get algae. what should i do

  6. avatar

    Sounds like nature is indeed taking it’s course! Ammonia spikes are normal as are nitrite spikes, in a few days the ammonia should drop, and you’re nitrates will rise. This signals that the cycle is settling and you can do a 20-25 percent water change and maybe add a couple more fish. Don’t go crazy, take it slow, monitor water quality, and you should be able to begin building your community! You may see minor fluctuations when testing, but it sounds like you’ll soon be ready to add fish. Let us know if you have any questions!

  7. avatar

    Hi Frank,
    I am transitioning some of my fish from a 55 gallon tank to a 75 gallon. The occupants (listed below) have been temporarily moved to some of my other tanks. At this moment, the 75 gallon is all set up, has new gravel, but the same filters that I did not clean. I have also added the initial dose of Cycle to speed up the process. The fish are over crowded in their temporary tanks, and I want to move them as quickly as possible to their new tank. My question is, how quickly can I safely do so? Thank you so much for your assistance.

    (1 pleco 14 inches long; 10 dwarf albino cory cats; 10 mollies; and 6 platys)

  8. avatar

    I have a saltwater set-up. First 2 weeks I ran the filter and didn’t worry too much about the testing. I have agronite rock/sand with the start as of to help balance PH within the water. Start of week 3 I put in about a 10 pound live rock 4 turbo snails and about a dozen small blue legged hermit crabs. The store never mentioned about ‘curing’ the rock before I dropped it in. Week 4 I bought 2 more chunks of rock and a clown fish. Week 5 I added another chunk of rock, have 4 pcs now about 10 lbs each. I also added a royal dottyback and a skunk shrip cleaner as well. Week six my PH level is about 7.8-8 which is bit low I think, and my ammonia was 0.25ppm nitrite #2, 0.25ppm mitrite#3, 5-10ppm. I also now have hundreds to thousands of iospods, maybe from over feeding my clown fish a bit, but the royal dottyback seems to be eating them. I assume the isopods are hitch hikers from the live rock as well now I also found what seems to be an emerald crab. Took a bit to get a decent look to identify him, he is small about same size as the hermit crabs. As with new growth I notice sphere like ‘things’ popping up and they also have 4 or 5 points on them. Almost like burrs you get from walking through a field with weeds. They have been attaching to various stuff in my tank. All in all everything seems to be going great. Looking for comments and opinions. Maybe with something new to add in the future that would blend in with my tank.

  9. avatar

    Jay, Sounds like your tank is doing well. Just be careful adding new live rock to a display tank, it can have short term effects on your water quality if it is not cured. Also keep an eye on how much you are feeding, Ideally you should have zero ammonia and nitrite in an established aquarium.

  10. avatar

    Can water changes be reduced if rain water, distilled water, or de-ionized water is used?

  11. avatar

    Hello TNflash, The water source wouldn’t really affect how frequently the water changes would need to be done. The changes may be more effective than from a water source that contains nitrates or phosphates, for example, but it wouldn’t change the amount of waste produced in the aquarium. Distilled and deionized water would also need to be buffered before it is added to most aquariums, depending on the type of aquarium and livestock in it. These other blog entries may help you in understanding this topic:
    The Importance of Water Changes in Aquarium Maintenance
    Pure Confusion – Finding the “Right” Water for Your Aquarium
    Treating the Treated – The Live Between Tap Water and Aquarium Water

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