Aquarium Nitrogen Cycle: Advanced Guide on the 3 Stages

Have you ever wondered why your newly added fish may have caused both your older or newly added fish to perish? Or, perhaps you are looking to fully understand the nitrogen cycle so that you can give your pet fish a healthy and long-lasting life. An incomplete or imbalanced aquarium nitrogen cycle may very well be the cause.

Describing the Aquarium Nitrogen Cycle

To describe the aquarium’s nitrogen cycle, it all begins in the presence of ammonia, either by adding a pure ammonia solution specifically made for aquariums, or organic waste or by adding live fish into a newly set up fish tank. Colonies of beneficial bacteria called Nitrosomonas and Nitrobacter bacteria will begin to grow naturally when ammonia and oxygen are present.

An aquarium’s filtration unit is the heart of the nitrogen cycle in aquariums, they are equipped with various bio-pads and bio-balls that filter out debris and provide a massive surface area for beneficial bacteria to colonize. Additionally, the substrate and other porous surfaces in your aquarium will also provide areas for beneficial bacteria to colonize.

This beneficial bacteria essentially breaks down ammonia to a lesser harmful compound called nitrite and then nitrite is further broken down into nitrate. Nitrate is relatively safe for fish unless the volume of nitrates accumulates, then it can also become lethal.

The aquarium’s nitrogen cycle performs optimally when dissolved oxygen levels are high and organic matter is low. Surface agitation caused by the filtration unit or underwater airstones promotes gas exchange, this agitation increases the rate at which oxygen dissolves in the water.

The more live fish and food added to an aquarium, the more organic waste will be produced, which in turn raises the aquarium’s ammonia, nitrite, and nitrate levels. However, an established colony of beneficial bacteria will continually grow to keep up with rising ammonia and nitrite levels.

Stage 1: What Causes Ammonia in Fish Tanks

Ammonia, which is produced by the decomposition of organic materials and is also excreted by the majority of fish, is the initial form and the start of the aquarium’s nitrogen cycle. Ammonia is present in the aquarium in two different forms: ammonium, which is not dangerous to fish unless levels are high, and ammonia, which is highly toxic and lethal to fish when found at levels of 1 ppm or greater.

The ratio of ammonia and ammonium will completely depend on the level of pH and temperature of water within the aquarium. As an illustration, 2% of the more harmful ammonia will be present in waters at 82°F (27.75°C) with a pH of 7.5 as opposed to 18% when the pH is increased to 8.5.

What does this mean, then? The levels of the more hazardous form of ammonia rise when the pH and temperature are higher while the levels of the less lethal form of ammonium fall. However, ammonia and ammonium are broken down equally to the less hazardous compound nitrite.

The chart below shows the total percent of ammonia found in varying pH and temperature parameters.

Ammonia vs ammonium chart with varying ph and temperature levels

Lowering the temperature and pH will result in less ammonia, which is advantageous for cycling a new fish tank or dealing with rising ammonia levels. It’ll give the aquarium more time to develop all of the beneficial bacteria that are required to break down both ammonia and ammonium.

There are many different indications of ammonia poisoning in fish that you should be aware of, including the following:

  • Fish swimming to the surface of the water and gasp for air
  • Gills rapidly moving or appearing to gasp for air
  • Red or purple gills
  • The fish becomes sluggish and lifeless
  • Loss of appetite
  • Body or fins with blood-red streaks
  • Swimming sideways or other erratic swimming behaviors
  • The fish is positioned on the aquarium’s floor, resting downwards with clenched fins

Stage 2: What Causes Nitrite in Aquariums

Ammonia and ammonium are converted to nitrite by Nitrosomonas bacteria, this process requires oxygen and produces acid which decreases pH. Nitrite is also a highly toxic compound and is lethal to fish at levels of 5 ppm or greater.

Stage 3: What Causes Nitrate in Aquariums

Nitrobacter bacteria will break down nitrite into nitrate; this conversion also needs oxygen and produces acid, which lowers pH. Nitrate also functions as a plant nutrient and, unless present in high concentrations, is not hazardous to fish.

We are left with the least hazardous byproduct of the nitrification process when ammonia has been converted to nitrite and nitrite to nitrate. Nitrate levels can only be decreased by aquatic plants, algae, corals, and routine water changes. Regular water changes also help with maintaining stable pH levels since each stage of the nitrogen cycle gradually lowers pH over time.

Although fish can tolerate small amounts of nitrates, the easiest way to describe how nitrates affect the health of fish is to imagine someone in an air-sealed room filled with smokers, and as each day passes, more smokers are added.

A few smokers may not entirely bother a person but as the smoke accumulates each day, short-term and long-term health issues may arise. As the accumulation of smoke persists without ventilation or any form of intervention, this will eventually lead to loss of life. Nitrates have a comparable impact on fish and should be kept at levels lower than 40 ppm, if not lower. In the wild, nitrate concentrations are often lower than 5 ppm.

Some may argue that slightly higher levels of nitrates are acceptable, and in a sense they are right. But, just like any pollutants that we may encounter, it is best to mitigate the amount of exposure to live a long and healthy life. Also, nitrates at 40 ppm or greater start to change most testing solutions to a deep red coloration, making it an ideal indicator that nitrates are too high.

Symptoms of prolonged exposure to high levels of nitrates are similar to ammonia poisoning in fish.

Smokey background

Aquarium Nitrogen Cycle: The Do’s and Don’ts

Consistency is key in keeping a stabilized nitrogen cycle. Daily and weekly routines should be created so that your water parameters are not fluctuating wildly but rather kept in balance.

Create a weekly cleaning and maintenance routine. It is preferable to perform smaller, more frequent water changes once the nitrogen cycle is established rather than larger, less frequent water changes. The chemistry of your aquarium’s water slightly alters as you change the water, and this might unintentionally have an impact on the health of your fish.

Never refill an aquarium without using a water conditioner since tap water contains chlorine and chloramines that are not only harmful to your fish but can also swiftly kill the beneficial bacteria that maintain the balance of your nitrogen cycle.

While regular tank cleaning and maintenance are crucial, you do not want to completely clean all of your aquarium’s substrate or filtration media in one session. This can potentially destroy the majority of the beneficial bacteria and restart the nitrogen cycle.

Select a different cleaning method during your weekly cleaning and maintenance routine when you decide to do a water change. For example, you might lightly rinse the filter media, clean the filter housing, or perform a deep cleaning of the substrate. When vacuuming the substrate, always do so in increments of 1/3 to 1/2 and never all at once.

During your cleaning and maintenance routine, it is advised to use a siphon to lightly clean the entire substrate’s surface in order to remove any leftover food or waste. The idea is to not upset too many beneficial microorganisms at once that are typically present within the substrate.

If you do need to replace the filter, do so in sections as most filtering units are made up of bio-foam, carbon, pads, bio balls, and other materials. Don’t replace all or multiple parts of a filtration unit at once.

Even in an established aquarium, adding too many fish at once will quickly raise ammonia and nitrite levels, which may very well cause your aquarium’s nitrogen cycle to stall or even collapse. Beneficial bacteria will increase as needed, but it takes time for them to develop and break down ammonia or nitrite concentrations that are higher than normal. It is a good idea to add additional fish in small batches rather than too many at once, the amount will largely depend on the size of your aquarium.

Ammonia, nitrite, and nitrate levels might rise over time as a result of overfeeding. It’s important to understand how much food your fish can consume in 3 to 5 minutes to avoid excess food from accumulating in and around your decor and substrate.


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