A Small Primer on Ammonia

The chemistry part of fishkeeping can be intimidating! One moment you’re setting up a brand-new fish tank, and the next moment there are fish gasping at the surface, all your test kits are turning green, and everyone at the fish store is throwing words like “ammonia poisoning” and “nitrification” at you. What even is ammonia and why is it such a big deal, anyways?

Hopefully, this article can provide a few tips on how to diagnose, eliminate, and prevent the buildup of ammonia—the big bad wolf of the hobby that constantly threatens to blow all of our glass and acrylic houses down.

What is ammonia?

In animals, ammonia is a metabolic waste produced by the constant breakdown of amino acids as they are digested inside of cells. Typically, ammonia leaves the bodies of aquatic animals through gills (fish) or skin (amphibians and many invertebrates). Ammonia is quite toxic to aquatic life, so fish need to continuously excrete it into the water around them, where it is diluted away. Our aquariums are significantly more densely stocked than lakes and rivers out in the wild, so our fish don’t always have the luxury of having their excreted ammonia immediately vanish into insignificant concentrations. This means that we should always be vigilant about ammonia levels in our tanks, since even a small spike can have disastrous outcomes!

How can I tell if my ammonia levels are spiking?

Unfortunately, there isn’t a specific visual cue that tells us our fish are suffering from ammonia poisoning. Because fish excrete ammonia out of their gills, excess ammonia will cause gill inflammation and can lead to the following symptoms:

  • Dark red, inflamed-looking gills
  • Gasping or hyperventilation

The general stress of ammonia poisoning can contribute to a more varied list of symptoms:

  • Lethargy and lying on the bottom of the tank
  • Erratic movements
  • Weight loss
  • Color loss (“washing out”)
  • Increased susceptibility to other diseases

Since many of these symptoms really don’t tell us a lot other than “this fish is suffering,” a good first response to anything going wrong in the aquarium is to test ammonia levels with a chemical test kit (liquid tests tend to be more accurate than the strips). Any ammonia level above 0 ppm (parts per million) is going to be a problem, and even 1 or 2 ppm can be very dangerous.

How is ammonia removed from the aquarium?

These days, learning about the aquarium nitrogen cycle is a rite of passage for most beginning hobbyists. It’s for a good reason, too! By understanding the nitrogen cycle, we can understand how ammonia is naturally detoxified and removed from our aquariums. Here’s the rundown:

Nitrifying (“nitrogen-eating”) bacteria grow on surfaces inside our aquariums. As ammonia is produced by animal waste and uneaten food, one species of this beneficial bacteria converts it into nitrite, an equally toxic compound. A second type of bacteria takes this nitrite and converts it into nitrate, which is much less dangerous than either of its precursors. Nothing in the tank can fully consume nitrate (though plants will use some as fertilizer), so it slowly builds up in the water over time. To prevent it from reaching harmful levels, we remove it from the aquarium through water changes. This is why it’s important to stay diligent with your water change schedule even if your aquarium isn’t visibly dirty!

In a well-established aquarium, ammonia and nitrite levels should stay at zero because these compounds are immediately converted away as fast as they are produced. Sometimes, an ammonia spike in your aquarium can overload the bacteria’s capabilities and you will find yourself with steadily rising ammonia levels. No need to panic if this is the case—you just have to physically remove ammonia from the aquarium through large water changes. Some water conditioners such as Seachem Prime claim to detoxify ammonia, but with a real lack of information regarding the actual mechanism of the product, it’s best to take these claims with a grain of salt. This possibility should be considered an added bonus that supplements, not replaces, water changes.

How can I cycle my tank?

When you “cycle” a tank, you are growing a suitably large population of bacteria that will be ready to handle all the ammonia your new fish will produce. We are not going to delve into the fiery, anecdote-laden debate over which method is best that rages across books and fish stores and online forums. Instead, we are just going to look at some ways you can combine the two ingredients (nitrifying bacteria and an ammonia source):

Here are some sources of nitrifying bacteria to colonize a new tank:

  • A tiny number of them already exist in even the newest tank—don’t worry about it!
  • Gravel or filter media from a mature tank
  • Commercially available bacterial supplements 

Choose just one of these ammonia sources to feed them with:

  • A pinch of fish food
  • A bit of raw shrimp
  • A few drops of liquid ammonia from the hardware store
  • A couple of hardy fish (not recommended as they will be exposed to excess ammonia in the water)

When the cycle is complete, you have grown enough bacteria to quickly convert any ammonia in the tank into nitrite and then nitrate. If you start off with a lot of bacteria, your cycle might finish in a week or two; if not, it may take up to a month. Either way, your goal is to grow a tiny bacterial colony into a thriving metropolis ready to process the entire bioload of a fully stocked tank.

Filter media is your aquarium’s lifeline.

Why doesn’t a big water change devastate the populations of beneficial bacteria you worked so hard to grow? As it turns out, there are actually very few nitrifying bacteria floating around in the water—most of them are stuck to various surfaces in the aquarium. They particularly like to colonize your filter media’s endless nooks and crannies, where the constant flow of water bathes them in a veritable buffet of nitrogenous compounds.

Some filter brands may instruct you to regularly replace the media, and at this point, it should be pretty clear why doing so is a horrible idea. Say goodbye to your lovingly cultivated, ammonia-destroying bacterial army! If your filter is getting a bit gunky, hang onto the bucket of old tank water after doing a water change, take out your filter media, and swish it around in the old water. Your bacteria have a pretty tight hold on media, but this will clear away all the sludge that has accumulated without hurting them. If the media has deteriorated beyond saving, gradually replace fractions of it instead of all at once so your bacteria have a chance to colonize their new media first.

Final remarks

Learning about how the different organisms in a fish tank interact with ammonia is often the first step to thinking about the aquarium as an entire interdependent ecosystem instead of just a “cage for fish.” The fundamentals of keeping any aquarium biologically and chemically balanced are the same. Tetras, koi, freshwater crabs—at the end of the day, aren’t we all just humble bacteria farmers?