Ammonia, Nitrite & Nitrate

The basic idea

Waste does not simply disappear.

Fish, shrimp, snails and other animals produce waste. Uneaten food, dead plant material and other organic matter also begin to break down inside the aquarium.

This process introduces nitrogen compounds into the water. In a mature aquarium, communities of microorganisms help process these compounds through what aquarists call the nitrogen cycle.

Ammonia

Ammonia is where the cycle begins.

Ammonia enters the aquarium as livestock produce waste and organic material breaks down. Uneaten food, dead leaves and dead animals can all contribute to the amount being produced.

In an established aquarium, ammonia should normally be processed quickly by the biological filter rather than accumulating in the water.

Ammonia toxicity

Temperature and pH affect how dangerous ammonia can be.

In aquarium water, ammonia exists in an equilibrium between un-ionised ammonia and ammonium. The un-ionised form is considerably more toxic to aquatic animals.

As pH and temperature increase, a greater proportion can exist in the more toxic un-ionised form. This is one reason an ammonia reading should be considered alongside the rest of the water conditions rather than viewed in isolation.

Nitrite

Nitrite is the next stage of the process.

Once ammonia-oxidising microorganisms become established, they convert ammonia into nitrite.

Nitrite is still dangerous to aquarium animals and should not be treated as a sign that cycling is finished.

During the cycling of a new aquarium, it is common to see ammonia begin to fall while nitrite rises. The system still needs time for the microorganisms that process nitrite to become established.

Nitrate

Nitrate is the end product most aquarists regularly manage.

Nitrite-oxidising microorganisms convert nitrite into nitrate. Nitrate is generally less immediately toxic than ammonia or nitrite, but that does not mean unlimited accumulation is harmless.

The amount considered suitable depends on the animals being kept, the aquarium and the wider water conditions. Sensitive livestock may require lower concentrations than hardier species.

Regular water changes, sensible feeding, removal of decomposing material and healthy plant growth can all help control nitrate.

Beneficial bacteria

Most of the biological filter lives on surfaces.

The microorganisms involved in nitrification colonise surfaces throughout the aquarium. Filter media provides particularly useful habitat because water carrying oxygen and nitrogen compounds passes through it continuously.

They can also live on substrate, decorations, plants and other surfaces. The important point is that they are not simply floating around in the aquarium water.

Cleaning the filter

Clean it when needed without trying to sterilise it.

Filter media eventually collects debris and may need gentle cleaning so water can continue flowing through it properly.

The goal is to remove excess debris, not make biological media look brand new. Avoid unnecessarily replacing established media simply because it has become discoloured.

If media genuinely needs replacing, changing part of it while leaving established media in place can help preserve biological filtration.

What cycling actually means

A cycled aquarium can process the waste being produced.

Cycling is not simply waiting a fixed number of days. The important part is establishing enough biological filtration to process the nitrogen waste entering the system.

That is why two aquariums started on the same day may not be ready at exactly the same time.

Water testing gives you evidence of what is happening instead of relying on the calendar alone.

Testing the cycle

Test results tell you what the aquarium is actually doing.

During cycling, testing ammonia, nitrite and nitrate helps you follow the development of biological filtration.

Rather than looking for one particular reading on one particular day, pay attention to the overall pattern. Ammonia should become increasingly well processed, followed by nitrite.

Before livestock are added, the aquarium should be capable of processing the expected waste without leaving harmful ammonia or nitrite behind.

• Follow the instructions supplied with your test kit.
• Check expiry dates and store testing equipment correctly.
• Measure samples carefully.
• Record results so changes are easier to spot.
• Repeat an unusual result before assuming it is correct.

Plants & the nitrogen cycle

Plants can use nitrogen, but they do not make cycling irrelevant.

Healthy aquarium plants take up nitrogen compounds as nutrients. Fast-growing plants can make a noticeable contribution to nutrient uptake in a well-planted aquarium.

However, plants should not be used as an excuse to ignore biological filtration or water testing. Growth rates change, plants can die back and livestock continue producing waste.

Plants and biological filtration work well together rather than being competing approaches.

Water changes

Water changes remove what the aquarium has accumulated.

Biological filtration converts nitrogen compounds, but it does not magically remove everything from the aquarium.

Regular partial water changes physically remove nitrate and other dissolved substances while giving you an opportunity to replenish the aquarium with appropriately prepared fresh water.

The right schedule depends on stocking, feeding, plant growth, aquarium size and measured water quality rather than one universal rule.

Feeding

Every bit of food eventually becomes part of the system.

Food that is eaten becomes waste. Food that is not eaten eventually decomposes. Either way, excessive feeding increases the amount of material the aquarium has to process.

Feeding appropriate portions is therefore not only about preventing obesity. It is also part of maintaining water quality.

Stocking

Biological filtration has limits.

A mature aquarium develops enough biological filtration to handle the amount of waste it normally receives. Adding many animals at once can suddenly increase that demand.

This is one reason gradual stocking is useful. It gives the biological community time to respond to a growing waste load.

Stocking should also consider adult animal size, behaviour, swimming space and species requirements — not just whether the filter can process the waste.

Cycle problems

An established aquarium can still run into trouble.

A mature tank is not permanently protected from ammonia or nitrite. Sudden changes can overwhelm or damage its biological filtration.

Possible causes include:

• A dead animal remaining unnoticed in the aquarium.
• Large amounts of uneaten food or decomposing material.
• A sudden increase in livestock.
• Loss or replacement of established filter media.
• Reduced filter flow or prolonged filter failure.
• Major disruption to the aquarium's biological surfaces.

Warning signs

Livestock behaviour can tell you something is wrong.

Poor water quality can cause changes in behaviour, but those signs are not specific enough to diagnose ammonia or nitrite by themselves.

Fish may breathe rapidly, remain near the surface, become unusually inactive or show other signs of distress. Shrimp may also behave abnormally when water conditions deteriorate.

If ammonia or nitrite appears

Protect the livestock first, then find the cause.

An unexpected ammonia or nitrite reading in a stocked aquarium should not be ignored.

Confirm the reading, check the aquarium for obvious causes and use appropriately prepared water changes to reduce harmful concentrations when necessary.

Check that the filter is operating correctly and look for excess food, dead livestock or decomposing organic matter. Continue monitoring the water while the aquarium recovers.

Managing nitrate

Nitrate still needs to be managed.

A functioning nitrogen cycle does not mean nitrate can simply be forgotten. In many aquariums, nitrate gradually accumulates as waste continues to be processed.

Regular partial water changes are one of the simplest ways to control it. Healthy aquarium plants can also use nitrogen as they grow.

Good maintenance, sensible stocking and avoiding excessive feeding all reduce the amount of waste entering the system in the first place.

Common mistakes

Cycling is simple in principle, but a few mistakes cause a lot of trouble.

• Adding livestock before the aquarium is ready.
• Assuming a tank is cycled simply because it has been running for a certain number of weeks.
• Thinking cloudy water automatically means the nitrogen cycle is complete.
• Replacing all established filter media at the same time.
• Overfeeding and allowing uneaten food to decompose.
• Adding a large amount of livestock to a newly established aquarium at once.
• Assuming nitrate is harmless because it is less immediately dangerous than ammonia or nitrite.
• Relying on livestock behaviour instead of actually testing the water.

Quick recap

Waste → ammonia → nitrite → nitrate.

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