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In the wild

In the wild, fish have large amounts of water continuously removing waste. Waste products become diluted to low concentrations.  The fish live in a continuously flushed environment.


In the aquarium

In aquariums and in small quantities of water nitrogenous waste has to be dealt with in that environment. It can take as little as a few hours for ammonia concentrations to reach toxic levels. The fish will start scratching and flicking on rocks and the gravel.  Within a few days the fish are sick. In a week fish are dying. You blame the local aquarium shop for the unhealthy fish and purchase more from a different shop. This shop owner suggests that you clean the tank and try again. The deathly cycle begins again.

A reputable aquarium should take time to advise new aquarists about the pitfalls and explain your duty of care.

The Aquarium Nitrogen Cycle

Some call it the biological cycle, the nitrification process or even the start-up cycle. They all are referring to the same cycle - The "Nitrogen Cycle". This very important cycle is the establishment of beneficial bacteria in the filter media that will help in the conversion of ammonia to nitrite and then the conversion of nitrite to nitrates. In this cycle waste and decaying matter is converted into less harmful substances which your fish can tolerate and plants can utilise. The cycling process normally takes anywhere from 2-6 weeks.

Just a note on filters: all filters regardless of the type have two functions

1.  To remove visible particles in the water and

2.  To provide a medium in which bacteria can grow and flourish.


Stage 1

All fish produce waste products. These nitrogenous waste products break down into ammonia (NH3), which is highly toxic to fish. Fortunately, several species of bacteria do this conversion for us. Some species convert ammonia (NH3) to nitrite (N02-), while others convert nitrite to nitrate (NO3-). During the cycling process, ammonia levels will go up and then suddenly plummet as the nitrite-forming bacteria take hold. Because nitrate-forming bacteria don't even begin to appear until nitrite is present in significant quantities, nitrite levels increase dramatically, continuing to rise as the continually produced ammonia is converted to nitrite. Once the nitrate-forming bacteria take hold, nitrite levels fall, nitrate levels rise, and the tank is fully cycled.

 Thus, cycling the tank refers to the process of establishing bacterial colonies in the filter bed that convert ammonia -> nitrite -> nitrate. The desired species of nitrifying bacteria are present everywhere (e.g., in the air). Therefore, once you have an ammonia source in your tank, it's only a matter of time before the desired bacteria establish a colony in your filter bed.

Ammonia is introduced into the aquarium via tropical fish waste and uneaten food. The tropical fish waste and excess food will break down into either ionised ammonium (NH4) or un-ionised ammonia (NH3). Ammonium is not harmful to tropical fish but ammonia is. Whether the material turns into ammonium or ammonia depends on the ph level of the water. If the ph is under 7, you will have ammonium. If the ph is 7 or higher you will have ammonia.


Stage 2

Soon, bacteria called nitrosomonas will develop and they will oxidize the ammonia in the tank, essentially eliminating it. The by-product of ammonia oxidation is Nitrites. So we no longer have ammonia in the tank, but we now have another toxin to deal with - Nitrites. Nitrites are just as toxic to tropical fish as ammonia. If you have a test kit, you should be able to see the nitrite levels rise around the end of the first or second week.

Stage 3

Bacteria called nitrobacter will develop and they will convert the nitrites into nitrates. Nitrates are not as harmful to tropical fish as ammonia or nitrites, but nitrate is still harmful in large amounts. The only way to rid your aquarium of nitrates is to perform partial water changes. Once your tank is established you will need to monitor your tank water for high nitrate levels and perform partial water changes as necessary.


What you need to do

Warning:  More fish means more ammonia production, increasing the stress on all fish and the likelihood of fish deaths. Once ammonia levels reach highly stressful or toxic levels, your tank has succumbed to ``New Tank Syndrome''; the tank has not yet fully cycled, and the accumulating ammonia has concentrations lethal to your fish.

Should ammonia levels become high during the cycling process, corrective measures will need to be taken to prevent fish deaths. Most likely, you will simply perform a sequence of partial water changes, thereby diluting ammonia to safer concentrations. ("Ammo-Lock'') safely neutralizes ammonia's toxicity. Biological filtration is still needed to convert the (neutralized) ammonia to nitrite and nitrate.

Speeding Up the Cycling Process

There are things you can do to speed along the process of cycling your aquarium.

1.  Increase the temperature of your aquarium water to 80ºF-82ºF (27ºC-28ºC)

    At temperatures below 70F, it takes even longer to cycle a tank. In comparison to other types of bacteria, nitrifying bacteria grow slowly.

    Under optimal conditions, it takes fully 15 hours for a colony to double in size!

    The most common way is to place one or two (emphasis on one or two) hardy and inexpensive fish in your aquarium.

2.  Don't overfeed them! More food means more ammonia!


3.  Take a cup of sand from this established aquarium and add it to yours.

4.  Put a cup of this sand in your filter temporarily.

5.  Borrow a filter from an established tank and run it in your tank for a few days.

6.  Squeeze the water out of a filter media of an established aquarium.

7.  Fill your aquarium with water taken from an established (larger) aquarium.

The basic idea is to find an established tank, take some of the bacteria out of it and place them in the new tank. Most filters have some sort of foam block or floss insert on which nitrifying bacteria attach. Borrowing all or part of such an insert and placing it in the new tank's filter gets things going more quickly.

If the established tank uses an undergravel filter, nitrifying bacteria will be attached to the gravel. Take some of the gravel (a cup or more) and hang it in a mesh bag in your filter (if you can), or lay it over the top of the gravel in the new tank (if it has an UGF).

If you have a box, sponge or corner filter, simply connect it to an established aquarium and let it run for a week or so. Bacteria in the water will establish a bed in the new filter. After a week, move the now ``seasoned'' filter to the new tank.

More recently, products containing colonies of nitrifying bacteria have become available at pet shops (e.g.,"Cycle''). In theory, adding the bacteria jump-starts the colonization process as above. However, nitrifying bacteria cannot live indefinitely without oxygen and food. Thus, the effectiveness of a product depends on its freshness and can be adversely effected by poor handling (e.g., overheating). Unfortunately, these products don't come with a freshness date, so there is no way to know how old they are.

How much ammonia is too much?

In an established tank, Ideally if a test kit is able to measure it, then it's too much.

The presence of detectable levels indicates that your bio filter is not working adequately, either because your tank has not yet cycled, or the filter is not functioning adequately (e.g., too small for fish load, clogged, etc.)

The exact concentration at which ammonia becomes toxic to fish varies among species; some are more tolerant than others. In addition, other factors like water temperature and chemistry play a significant role. For example, ammonia (NH3) continually changes to ammonium (NH4+) and vice versa, with the relative concentrations of each depending on the water's temperature and pH. Ammonia is extremely toxic; ammonium is relatively harmless. At higher temperatures and pH, more of the nitrogen is in the toxic ammonia form than at lower pH.

The following chart gives the maximum long-term level of ammonia-N in mg/L (ppm) that can be considered safe at a given temperature and pH. Again, note that a tank with an established biological filter will have no detectable ammonia; this chart is provided only for emergency purposes. If your levels approach or exceed the levels shown, take emergency action IMMEDIATELY.

It is imperative that you address the problem (filter) in addition to the symptoms

       pH             Temperature


20C (68F)

25C  (77F)

















Now that you have your biological filter established you need to take care that it doesn't die off just like you do for every other living things in your aquarium. You should give it as much consideration as you do the other living things in your aquarium, the fish and plants.

Take care when doing maintenance on your filter not to kill off or remove too many of these bacteria that you have worked so hard to get established there. Also take care and don't try to increase your fish load too quickly.

Every time you add new fish and as fish grow it takes some time for the biological filter to adjust to the new conditions and most of the time it will do so without any problems.

What you want to avoid is suddenly dumping in twice as many fish as you already have in a lightly stocked aquarium and expect that since you have already cycled your aquarium you won't have any problems. While you won't see near the levels of ammonia and nitrate that you did while cycling it is common to see slightly increase levels. Also you will find that for about the first month or so after completing the initial cycle your biological filter will be particularly venerable to sudden changes in the fish load.

After that first month after the cycle the aquarium is really pretty stable and as long as you keep up with your aquarium maintenance it should remain so.



NEVER totally wash and clean an established aquarium if possible.

However if you have to do so, try the following procedure, which will save your colony of beneficial bacteria from


  1. Siphon out all the water (half to put back in the aquarium) and half for rinsing as below.
  2. Remove the filter and keep it wet in the water to be returned to the aquarium water.

  3. Do not clean the filter.

  4. Remove the sand, rinse in the water set asside as in (1)

  5. Now wash tank, stones etc.

  6. After you reset the tank, pour back the water saved in step 1

  7. Put back the filter without cleaning.

  8. Top up the aquarium with fresh water treated with the appropriate amount of chlorine neutraliser and conditioner.

  9. Change water after a few weeks.

NEVER   Clean out a filter media (sponge) completely. Rinse the filter media gently in clean water to remove surface           blockage and re- install. This will retain most of the beneficial bacteria.

NEVER    Add chlorinated water directly to your aquarium. Chlorine is added to water to kill harmful bacteria, but it also kills beneficial bacteria very effectively. Use a chlorine remover, or allow water to sit in a bucket with an aerator for some time before adding it to your aquarium. Water stored in a sump or overhead tank will lose all chlorine over time.

NEVER   Add a lot of new fish to your tank in one go. The bacteria colony will not be able to handle the sudden increase in load. Buy and add new fish a few at a time. Now you know why fish suddenly start dying after you have added a new lot of new fish.

NEVER   Increase the feed amount to the fish suddenly - the bacteria might not be able to take the extra load of excrement.

To prevent overfeeding when you are leaving town for a few days, put the daily feed amount in small packets with instructions  to the person who is looking after your fish