How To Lower Ammonia in An Aquarium

Section 1: Understanding Ammonia and the Nitrogen Cycle

This topic may feel a bit dry, but it’s essential for every aquarist.

1. What is ammonia? (In case you forgot from high school chemistry)

Ammonia is a naturally occurring chemical in every aquarium. It’s produced by the decomposition of organic matter, including fish waste (feces and urine), uneaten food, and decaying plant material.

While a full discussion of the nitrogen cycle isn’t the focus of this article—plenty of resources cover it well—it’s important to know that nitrifying bacteria process ammonia into less harmful substances.

2. Does your aquarium have high ammonia levels?

High ammonia levels occur when there aren’t enough nitrifying bacteria to handle the aquarium’s waste load. This waste load includes all decomposing material in the tank: fish waste, leftover food, and sometimes a deceased fish you haven’t yet discovered. (I once lost a fish due to a large, unnoticed dead snail, which caused a sudden spike!)

3. Danger, Danger! Ammonia!

Ammonia is highly toxic to fish and can kill them quickly—I’ve seen it happen in as little as 24 hours.

Analogy: Imagine being trapped in a room filled with concentrated ammonia gas. The fumes would severely injure you, potentially causing blindness, skin burns, or lung damage. This is the same danger your fish face when ammonia levels rise.

Section 2: Signs of Ammonia

4. Sniffing out the usual suspect — Ammonia

If your fish look like they’re starring in a crime drama called “CSI: Aquarium,” you probably have an ammonia problem. (A little AI flair to keep things lively!)

The clearest clue that ammonia is present is sudden fish death. The fish won’t show signs of illness beforehand—they’ll simply die. Survivors may display alarming behaviors such as “spinning and dancing” (not the fun kind), gasping at the surface, or showing inflamed gills. If you notice any of these symptoms, test your water immediately for ammonia.

How to confirm

Use a chemical test kit. You can purchase one from your local fish store, or bring in a water sample and ask them to test it for you.

Section 3: Where does the ammonia come from?

There are several sources of ammonia in your aquarium. The most common include:

5. Fish waste and urine

Think about it—aquarium fish live in their own toilet. The primary source of ammonia in any stocked tank is fish waste. As fish eat and digest food, they naturally excrete waste and urine, both of which break down into ammonia. This process is part of the nitrogen cycle, which occurs in every aquarium. Even in a well‑maintained tank, waste is constantly being produced.

6. Uneaten food

Another major contributor to ammonia is leftover food. When fish don’t consume all the food provided, the uneaten food sinks to the bottom and begins to decompose. Over time, this decaying matter turns into mulm—the dark, cloudy debris you may notice when stirring the gravel. As food decays into mulm, the process releases ammonia into the water.

7. Decaying plant matter

Healthy plants can help absorb ammonia, but when leaves or stems die, they break down into mulm. Just like uneaten food, this decomposition process releases ammonia into the water. Regularly trimming dead leaves and removing decaying plant matter is an easy way to prevent sudden spikes.

8. Undiscovered dead fish or snails

Although less common, a hidden dead fish or snail can cause a sudden surge in ammonia. Even a single large snail decomposing unnoticed can overwhelm the system. It’s a good habit to check your aquarium during feeding time to make sure all inhabitants are accounted for and no problems are lurking.

Here are the filtration systems I use or have used:

1. A hang on or canister filter with hard and soft filter media. Soft media is usually polyester filter fiber (used to stuff pillows) in some form. Hard media comes in various shapes including balls, beads, and rings. Hard media can be made of plastic or ceramic. I use ceramic media formed as small, fat, one inch rings.

Be careful when cleaning your filter to protect the filter media and therefore protect the beneficial bacteria.The filter fiber will need to be replaced occasionally so having the hard media acts as an additional backup.

As an FYI, I never, ever clean my hard media. It doesn’t need it and the bacteria on it are too valuable to risk them going down the drain.

2. I’ve had outstanding success using sponge filters run by powerheads. The sponges are fantastic places for the bacteria to grow. Sponge filters can support so much growth they actually become clogged with good bacteria (and debris).

Make sure to be careful when cleaning the sponge filter so you don’t kill the bacteria. As with other filters, have a second filter running so that if you harm the bacteria when cleaning one sponge, the other can take up the ammonia load for a while.

3. Undergravel filters are amazing at growing beneficial bacteria. They work by pulling water down through the gravel, then up into the aquarium again. The gravel supports a huge load of nitrifying bacteria. For beginning aquarists, this would be a good and maybe best choice. I haven’t used an undergravel filter in years, though. They interfere with the growth of my aquarium plants.

Solution #2 to get rid of ammonia in your aquarium naturally.

Use massive water changes:

To save your fish, a 90 or 95% water change would not be too much.

Change a large percentage of the water in the tank daily. I would change out at least 90% of the water each time until your nitrifying bacteria catches up and can eliminate the ammonia naturally. Treat the water that goes back into the tank with a chlorine & chloramine remover made for aquarium. Your water company adds chlorine and chloramine to your tap water to kill bacteria. You can see why this would be a problem.

Solution #3 to get rid of ammonia in your aquarium naturally.

Remove the fish from your aquarium while you wait for the ammonia level to drop to zero:

Move the fish from the first tank into a container that is heated and oxygenated. Call this container your hospital tank. The fish can heal there while you fix the ammonia problem in your aquarium.

* Check the ammonia level in the new container daily. You don’t want the same problem in your hospital tank as you have in your first tank.

* Try hard to under-feed the hospitalized fish to keep the ammonia level down while they are in the new container. Personally, I would wait at least five or six days, if needed, before feeding the fish. At least until they are back in the old aquarium.

* Do water changes in the hospital container if or as needed.

In your old tank, you are now waiting for the numbers of nitrifying bacteria to become large enough to fix the ammonia problem. As mentioned earlier in this article, make sure you have at least two filter systems going in that tank.

* Check the old aquarium’s ammonia levels daily.

* When the ammonia reaches zero, put 10% of your fish back into your old aquarium.

* Check the ammonia in the aquarium the next day. If it is not zero, wait a day and check again. When the ammonia is zero, add a few more fish.

* Repeat the process until all of your fish are back in the aquarium.

* Keep two filtration systems going at all times in the aquarium for natural protection against ammonia in the future.

Whether you are setting up a new aquarium or have one up and running already, always have at least two filter systems running. “An ounce of prevention is worth a pound of cure” couldn’t be more true than when discussing natural removal of ammonia in fish aquariums.

Now go make your fish happy and healthy, by getting rid of ammonia in your aquarium naturally.

Male and female zebra danios in my 30 gallon aquarium

My 30 gallon – male and female zebra danios