Ammonia, in the aquarium hobby, refers to two chemical compounds, free ammonia (NH3) and ammonium (NH4+) together. Ammonia is a food source for nitrifying bacteria and is toxic to fish, amphibians and invertebrates. It is a key input to the The Nitrogen Cycle and an important parameter to measure when cycling a new tank.
What is it?
Free ammonia is a chemical compound of nitrogen and hydrogen with the formula NH3. Technically ammonia in water is called Ammonium hydroxide. In the aquarium hobby the term ammonia also refers to an ionized form called ammonium (NH4+). These are held in equilibrium in the water [Citation needed]. 'Total ammonia' (TA) or 'Total ammonia nitrogen' (TAN) refers to the total concentration of both NH3 and NH4+ in the aquarium water.
Where you have Ammonia, you will also have Ammonium. The ratio of one to the other varies on pH and water temperature. So it is important to know these two readings when measuring Ammonia in your tank to gauge how serious the Ammonia levels are. See the Links section for a Toxic Ammonia calculator. Here is a table showing the varying levels of ammonia against ammonium.
|Temp C/F||pH 6.5||pH 7.0||pH 7.5||pH 7.7||pH 8.0||pH 8.5|
Sources of Ammonia
- Fish excrete ammonia as a waste byproduct of metabolism. In particular, fish excrete free ammonia from their gills and ammonium in their urine. It is suspected invertebrates excrete ammonia in some form as well. The amount of ammonia excreted will vary with amount of food eaten.
- Decaying organic material from dead animals and uneaten food. As the material decomposes, nitrogen is released which is converted into ammonia by bacteria.
- tap water
- salt mixes
Testing for Ammonia
The concentration of ammonia in water is easily measured with widely available test kits. There are two common methods for measuring ammonia: Nessler measures total ammonia (NH3 and NH4+)  and Salicylate measures free ammonia (NH3) . A test kit will use one or both methods. In the marine hobby if a test kit does not explicitly state it measures free ammonia then it is likely uses the Nessler method and measures total ammonia.
Some Water conditioners transform free ammonia (NH3) into ammonium (NH4+). As a result, Salicylate test kits will show a decrease in free ammonia while the Nessler test kits will not show any change in total ammonia.
The typical unit of measure is ppm (parts per million). In seawater ppm and mg/L are interchangeably since 1 ppm ammonia = 1.03 mg/L ammonia.
- Free ammonia is highly toxic to aquatic life. It kills in aquariums at very low amounts. Any level above 0.02 mg/l (ppm) is considered harmful.
- Ammonium may be toxic to marine fish, especially if the pH differs significantly from natural seawater (e.g. during shipping) 
- Free ammonia causes gill damage, internal organ damage and eventually skin damage and death. Typical symptoms include:
- ragged or frayed fins
- cloudy eyes
- rapid gilling
- lack of appetite
- more susceptible to disease
- In general, ammonia is more toxic at higher alkaline pH values and as the temperature of the water increases.
- Ammonia is not toxic to plants in levels that would cause distress to fish, indeed of those plants tested, most preferred ammonia or ammonium as a food to nitrate .
- Rough guide to toxic levels of free ammonia:
- 0.020 to 0.049 (ppm) is considered 'tolerated' but will cause long term harm to its growth, immune system, health, etc. especially to eggs or very young animals.
- 0.050 to 0.199 (ppm) is perhaps tolerated for only a few days and is very harmful.
- 0.200 to 0.499 (ppm) is perhaps tolerated for a day or two and will probably kill.
- 0.500+ (ppm) is deadly and will probably kill within a day.
- Individual species of fish, amphibians, invertebrates etc. vary enormously on their tolerances of low levels of ammonia and the issue is made further complicated as young are far more susceptible to ammonia than older animals. 
- In nitrogen sensitive fish like Trout, ammonia is about 6x more toxic than nitrite and about 13,300x more toxic than nitrate 
A healthy aquarium should contain enough ammonia consumers to consume all ammonia produced naturally by the system. These consumers come in two forms:
- Nitrifying bacteria will consume ammonia and convert it to the less toxic nitrite chemical. However, it can take many weeks to establish the bacteria in large enough quantities in a new tank.
- Plants in a tank will soak up ammonia in order to grow. This works well but can take time.
When detectable levels of ammonia are found, these short term but immediate options are available:
- Perform a water change. This dilutes the total ammonia levels quickly and cheaply.
- Add a water conditioner that neutralizes ammonia. These can be expensive and can cause false readings in some test kits. But are virtually instantaneous in use and less work. Be sure to buy a product that specifically says it detoxifies or neutralizes ammonia. Some water conditioners may create ammonia as a byproduct of removing chlorine or chloramine.
- Add special resins or rocks which soak up the ammonia. These are reusable and relatively cheap. Typical resin product names based on zeolite are Ammo-Chip or Ammo-Carb.
- Ammonia in a freshwater aquarium can be rendered less toxic by adding a small quantity of salt to the water. See Salt article.
- Some algae consume ammonia so ammmonia in an aquarium can cause a bloom.
It is useful to add ammonia to a new tank in order to cycle it before adding any animals. There are products on the market which sell diluted ammonia as a cleaning agent. It is important to only buy a product with no additives (surfactants, perfumes, and colourants, etc.) that may pollute the water with other toxins. Usually the cheapest brands have the lowest additives.
- See article - Fishless cycling for details.
- UK - Kleen Off
- USA - "Pure" Ammonia is sold in the US at WalMart as "Clear Ammonia", and at Ace Hardware as item "10183A Ammonia- Janitorial Strength Formula".
- EU - please add one
- Ammonia Test Kits: Nessler vs. Salicylate
- Ammonia Tests http://www.chemetrics.com/pdf/Ammonia.pdf
- Mechanisms of Ammonia Excretion by Marine Fish
- PLANTS and BIOLOGICAL FILTRATION by Diana Walstad
- US Environmental Protection Agency. Ambient Water Quality Criteria for Ammonia, (EPA 440/5-85-001) 2009. 
- Glodek, Garrett S. "Ammonia in the Closed System Aquarium," FAMA, June 1991.
- Barr Report (subscription required) - Fish Waste and Macrophytes paper page 9 - March 2007
- Ammonia by Wikipedia
- The Krib - Ammonia Toxicity to Freshwater Fish
- Ammonia in aquariums and safe levels by the OATA
- Ammonia in Aquatic Systems by Ruth Francis-Floyd, Craig Watson, Denise Petty, and Deborah B. Pouder of the University of Florida
- How to calculate the level of free ammonia at certain pH and temperature in water by Professor James E. Alleman (Archived link March 2005)
- Toxic Free Ammonia level Calculator (select 'Aquarium Tools' from the list of Tools on the page)
- Ammonia in Fish Ponds by Robert M. Durborow, David M. Crosby and Martin W. Brunson. SRAC June 1997 (Archived link)
- Koi and Water Garden Society - Free Ammonia calculator
- The ammonia/ammonium equilibrium by Mr. Nielsen. (Archived 2008)