Aquarium Nitrogen Cycle

How an Aquarium Cycles

Nitrogen Cycle
Shirlie L Sharpe

Call it cycling, nitrification, biological cycle, startup cycle, break-in cycle, or the nitrogen cycle. No matter what name you use, every newly set up aquarium goes through a process of establishing beneficial bacterial colonies. Older aquariums also go through periods during which the bacterial colonies fluctuate. Failure to understand this process is the largest contributing factor to the loss of fish in new aquariums. Learning what it is, and how to deal with critical periods during the nitrogen cycle, will greatly increase your chances of successful fish keeping.

The Waste Problem

Unlike nature, an aquarium is a closed environment. All the wastes excreted by the fish, uneaten food, and decaying plants stay inside the tank. If nothing eliminated those wastes, your beautiful aquarium would turn into a cesspool in no time at all.

Actually, for a short period of time, a new aquarium does become a toxic cesspool. The water may look clear, but don't be fooled. It's loaded with toxins, much like a septic tank. Sounds awful, doesn't it? Fortunately, bacteria that are capable of converting wastes to safer by-products begin growing in the aquarium as soon as fish are added. Unfortunately, they grow slowly and there aren't enough bacteria to eliminate all the toxins immediately, so for a period of several weeks to a month or more, your fish are at risk. This is the period of new-tank cycling.

However, you need not lose the fish. Armed with an understanding of how the nitrogen cycle works and knowing the proper steps to take, you can sail through the break-in cycle with very few problems.

Stages of the Nitrogen Cycle

There are three stages of the nitrogen cycle, each of which presents different challenges.

Initial stage

The cycle begins when fish are introduced to the aquarium. Their feces, urine, as well as any uneaten food, are quickly broken down into either ionized or un-ionized ammonia. The ionized form, Ammonium (NH4+), is present if the pH is below 7, and is less toxic to fish.


The un-ionized form, ammonia (NH3), is present if the pH is 7 or above, and is highly toxic to fish. Any amount of un-ionized ammonia (NH3) is dangerous, however, once the levels reach 1 mg/L, the fish are in grave danger. Ammonia usually begins rising by the third day after introducing fish.

Second Stage

During this stage Nitrosomonas and Nitrospira species of bacteria have multiplied enough to oxidize the ammonia, thus eliminating it. However, the by-product of ammonia oxidation is nitrite (NO2-), which is also highly toxic to fish.


Nitrite levels as low as .10 mg/L are toxic and could be lethal to some fish. Nitrite usually begins rising by the end of the first week after introducing fish.

Third Stage

In the last stage of the cycle, Nitrobacter bacteria convert the nitrite into nitrate (NO3-). Nitrate is not toxic to most fish at low to moderate levels. Routine partial water changes will keep the nitrate levels within the safe range. Established aquariums should be tested for nitrate every month to ensure that levels are not becoming extremely high.

Water Additives

Now that you know what is happening, what should you do? Simple steps such as water testing and changing the water will help you manage the nitrogen cycle without losing your fish.

Using ammonia binding chemicals from the fish store will also detoxify the ammonia produced in a newly established aquarium, keeping the fish safe. Adding one to three teaspoons of aquarium salt per gallon of water will reduce the toxicity of nitrite to the fish.

Getting bacteria starters from the aquarium store to add to your aquarium will speed up the cycling process, cutting it down from 4 to 6 weeks to half that time, or even less. These products add heterotrophic bacteria that break down wastes, and some even add enzymes that help in the nitrogen cycle.

Article Sources
The Spruce Pets uses only high-quality sources, including peer-reviewed studies, to support the facts within our articles. Read our editorial process to learn more about how we fact-check and keep our content accurate, reliable, and trustworthy.
  1. Ammonia in Aquatic Systems. University of Florida Institute of Food and Agricultural Sciences.

  2. Aquarium Water Quality: Nitrogen Cycle. Florida Department of Agriculture and Consumer Services.