Published on 26 February 2024 at 23:45

Ammonia is formed from the metabolism of protein and is the major waste product of fish. The majority of ammonia from fish is excreted through the gills, with relatively little being lost through urine and feces. Ammonia is also formed as uneaten feed or other organic matter in an aquarium decomposes. High concentrations of ammonia in the water make it difficult for fish to eliminate ammonia from their bodies. This buildup of ammonia can cause stress, gill and internal organ damage, and eventually death.

Total ammonia is comprised of two components: un-ionized ammonia (NH3) and ionized ammonia (NH4+). Un-ionized ammonia is extremely toxic to fish whereas ionized ammonia is not. The proportion of un-ionized to ionized ammonia shifts in relation to pH and water temperature. As pH or temperature increases, more of the ammonia shifts to the un-ionized, toxic form. Un-ionized ammonia begins causing gill damage at approximately 0.05 mg/L and death at approximately 2.0 mg/L. Keep in mind that most test kits measure total ammonia and not un-ionized ammonia but may make no reference to the difference. A table is used to calculate the portion of un-ionized ammonia from total ammonia.

Ammonia is removed from an aquarium system through the use of a biofilter. The biofilter provides a substrate on which nitrifying bacteria grow. These nitrifying bacteria consume ammonia and produce nitrite, which is also toxic to fish. Other nitrifying bacteria in the biofilter consume nitrite and produce nitrate. Nitrate is not toxic to most freshwater fish, except in high levels, and can be reduced sufficiently through periodic water changes. Some nitrate will also be utilized by plants. In natural systems and some aquarium systems, nitrate is converted to nitrogen gas by denitrifying bacteria. This conversion from ammonia to nitrite to nitrate to nitrogen gas is known as the nitrogen cycle.

Nitrifying bacteria, although naturally present in the environment, will take time to accumulate on biofilter media before they can efficiently remove all of the wastes produced by the fish. Setting up a tank and stocking it full of fish the same day, or even within a week or two, is a sure recipe for disaster. The bacteria in the biofilter can require three to eight weeks to cycle (i.e., become established) at 77-80 degrees F; even more time may be required at cooler temperatures. Aquarists can begin this cycling process by utilizing one or more of the following methods:

  • Adding clear, non-sudsy household ammonia directly to the system to a level of 23 mg/L adding a few individuals of a species of fish that can handle the initial high ammonia and nitrite levels before adding the final species to be held.
  • Seeding the system/biofilter with water or substrate containing bacteria from a "healthy" established system.
  • Seeding the system with bacteria from a reputable commercial source.

As a biofilter cycles, ammonia will rise until sufficient nitrifying bacteria are present to consume the ammonia and convert it to nitrite. Ammonia levels will then begin to decrease while nitrite levels increase. Nitrite levels will continue to increase until sufficient bacteria are present to consume the nitrite and convert it to nitrate. Unless many plants are present, nitrate levels will rise slowly until a water change is performed. Ammonia and nitrite tests should be conducted every few days until the ammonia level and then nitrite level spike and lower (i.e., cycle). Tanks that are stocked before the biofilter is functioning properly will often become cloudy because of heavy non-nitrifying bacterial blooms.

After the cycling period, ammonia should be tested once per week. Once established, a well-managed aquarium should have no detectable levels of ammonia. If ammonia is present, management of the aquarium should be evaluated to ensure:

  • The biofilter is large enough.
  • The biofilter does not need cleaning.
  • The aquarist is not overfeeding (based on what the biofilter can handle, not what the fish will consume).
  • The tank is not overstocked.
  • The tank is not excessively dirty.
  • The biofilter is not too clean (vigorous cleaning of the biofilter will remove nitrifying bacteria).
  • The alkalinity or pH have not dropped and negatively affected the biofilter
  • No chemicals have been used that have killed the bacteria in the biofilter.