The nitrogen cycle in a pond: ammonia, nitrites, and nitrates explained simply

Pond fish live in their own waste. Put that way, it sounds unappealing, but that is exactly what happens: every day, they release nitrogen into the water, and every day, an invisible army of bacteria transforms it. When this chain works, no one notices it. When it falters, the fish cling to the surface, their fins close up, and the water deteriorates. The nitrogen cycle is the underlying mechanism of every populated pond: understanding it means understanding why we filter, why we aerate, and why we cannot feed as we please. This guide explains it step by step, without unnecessary jargon, and shows how each link affects your maintenance.

Where the pond's nitrogen comes from

Nitrogen is a component of all proteins. It enters the pond mainly through food and leaves it in the form of waste. Fish do not produce urea like mammals: most of their nitrogen is excreted directly through the gills, in the form of ammonia, with only a small portion passing through their feces.

The other sources are more diffuse but have a significant impact over time:

• Uneaten food, which decomposes on the bottom or in the filter.
• Leaves, faded flowers, and dead plants, especially in autumn.
• Mud, a true reservoir of organic nitrogen that mineralizes slowly.
• Runoff from a fertilized lawn or vegetable garden.
• Rain, which brings in a small amount of dissolved nitrogen.

The practical rule that follows is simple: the amount of nitrogen circulating in your pond depends first and foremost on the amount of food you distribute. That is why an overcrowded or overfed pond always ends up with water problems, even with a large filter.

Ammonia and ammonium: the role of pH

What tests call “ammonia” or “NH₄ » actually covers two chemical forms in equilibrium in water:

• Ammonium (NH₄⁺), the ionized form, which is relatively non-toxic to fish.
• Free ammonia (NH₃), the un-ionized form, which easily passes through the gills and is highly toxic.

The proportion of each depends mainly on pH and, to a lesser extent, on temperature. The more alkaline and warmer the water, the greater the proportion of toxic ammonia. Tables published in the aquaculture literature (notably reproduced by Boyd and Tucker) give the following approximate values:

In practical terms, the same measurement of 0.5 mg/l of total ammonium does not mean the same thing in a pond at pH 7 on a cool morning as it does in a pond at pH 9 on a summer afternoon. A pond rich in algae can see its pH rise above 9 at the end of a sunny day, because photosynthesis consumes CO₂. This is when ammonia causes the most damage. Hence the importance of always reading an ammonium value together with the pH measured at the same time.

Nitrites: the dangerous spike

The first stage of nitrification is carried out by bacteria known as ammonia-oxidizing bacteria. The historically described genus is Nitrosomonas, but we now know that other groups, including archaea, also participate in this stage. They obtain their energy by oxidizing ammonium into nitrite (NO₂^-).

Nitrite is a stealthy poison. Absorbed through the gills, it transforms hemoglobin into methemoglobin, a form unable to transport oxygen. The blood takes on a brownish color, hence the name “brown blood disease” used in fish pathology (Noga, Fish Disease). The fish suffocates even though the water contains oxygen: it stays at the surface, breathes rapidly, and becomes lethargic.

Nitrites are mainly a problem in three situations:

• A new pond, in which the bacteria involved in the second stage have not yet become established. The nitrite spike then follows the ammonia spike by a few days to a few weeks.
• A disturbed filter: overly vigorous cleaning, rinsing with chlorinated water, prolonged pump shutdown.
• A sudden overload: adding many fish at once, heavy feeding in spring while the filter has barely restarted.

Chlorides present in the water compete with nitrite at the gills, which explains why very soft water makes fish more sensitive. For an action plan in the event of a spike, refer to a treatment guide; here, remember above all that a measurable nitrite level always indicates an imbalance in the filter.

Nitrates: food for algae

The second step is carried out by nitrite-oxidizing bacteria, of the genera Nitrobacter and especially Nitrospira in freshwater filters. They convert nitrite into nitrate (NO₃^-). Some Nitrospira strains are even capable of carrying out both steps on their own, which microbiologists call “comammox.”

Nitrate is much less toxic than the two previous forms. Fish tolerate high concentrations without visible signs, even though persistently very high levels are associated with chronic stress. Its real problem lies elsewhere: it is a fertilizer. Along with phosphates and light, it feeds suspended algae (green water) and filamentous algae.

In a pond with neither enough plants nor water renewal, nitrates accumulate season after season. This is often the missing link when wondering why “the water tests perfectly but is still green”: ammonia and nitrite tests read zero because the filter is working well, but all this converted nitrogen feeds the algae.

Nitrifying bacteria and oxygen

Nitrifying bacteria do not swim freely in the water: they live in a biofilm, a thin, slimy layer that covers the foam, filter media, stones, pond liner, and even plant stems. The greater the colonizable surface area, the higher the treatment capacity. This is the whole purpose of biological media with a high specific surface area in a filter.

These bacteria have three main requirements:

The connection with KH is often overlooked. In a heavily stocked pond filled with rainwater, nitrification gradually consumes carbonates, the pH becomes unstable and may drop suddenly, which in turn stops the bacteria. The article How to increase the KH of a pond or water garden? details the possible corrections.

Oxygen is the most common limiting factor in summer: warm water dissolves less of it, fish consume more, and so do filter bacteria. Supplemental aeration during hot nights relieves the entire system. The guide to choosing an aerator helps size an air pump.

Denitrification and the role of plants

Once nitrogen has been converted into nitrate, it does not disappear. It can leave the water in three ways.

Absorption by plants. Submerged plants, marginal plants, water lilies and, it must be said, algae, take up ammonium and nitrates to make their own proteins. Dense, actively growing vegetation is a direct competitor to algae. This is what Scheffer's theory of alternative stable states in shallow lakes describes on a large scale: a body of water dominated by macrophytes tends to remain clear, while one dominated by phytoplankton tends to remain cloudy. For species selection, see the list of filtering aquatic plants.

Denitrification. In oxygen-free zones, at the heart of sludge or at the bottom of a clogged filter, other bacteria breathe nitrate instead of oxygen and convert it into nitrogen gas, which escapes into the air. This process genuinely removes nitrogen from the system, but it has a downside: anoxic zones also produce undesirable compounds, and thick sludge releases phosphorus. So we do not seek to encourage denitrification by letting the pond become silted up.

Water replacement and material export. Replacing some of the water, removing sludge, pruning plants and removing plant waste: all of this physically exports nitrogen. A pruned plant thrown into the compost takes with it the nitrogen it has stored.

What the cycle changes in daily maintenance

Once the mechanism is understood, most of the “rules” of pond maintenance become logical. Here they are linked to their purpose.

1. Feed according to temperature. As the water cools, bacteria slow down: the same amount of food then produces more ammonia than the filter can process. Reduce feeding in autumn and resume gradually in spring.
2. Introduce fish gradually. A bacterial population is sized according to the load it receives. Doubling the load overnight creates a deficit lasting several days.
3. Clean the filter with pond water. Chlorine in tap water and overly thorough cleaning destroy the biofilm. Rinse the media in a bucket of pond water, and never all of them at once.
4. Do not switch off the pump for hours. Without circulation, the filter lacks oxygen, some of the bacteria die, and when it restarts, stagnant water from the filter can send a burst of undesirable compounds back into the pond.
5. Measure, especially during high-risk periods. New pond, spring, heatwave, adding fish, after a treatment: these are the times to test ammonium, nitrites and pH. The article How to analyze the water in my pond or ornamental pond? explains the method.
6. Plant and prune. Plants absorb nitrates; pruning them exports nitrogen from the pond.
7. Help the filter when it restarts. In spring or after an incident, adding selected nitrifying bacteria can shorten the period of imbalance. It does not replace oxygen or a reasonable load.

Test reading guidelines

The values below are commonly accepted guidelines for ornamental ponds, to be interpreted alongside pH and temperature:

• Total ammonium: ideally undetectable; any measurable value warrants checking the pH.
• Nitrites: ideally undetectable; a few tenths of a mg/l already indicate an overloaded filter.
• Nitrates: as low as possible; above a few dozen mg/l, algae have a buffet at their disposal.

Also read

To learn more about the actors in the cycle: The importance of bacteria in your pond: the complete guide.

READ THE ARTICLE

Frequently asked questions

— How long does it take for the nitrogen cycle to become established?

As a general estimate, four to six weeks in water above 15 °C, longer in cool weather. Bacterial seeding and a gradual load shorten this phase.

— Why is ammonia more dangerous in summer?

Because the proportion of free ammonia, the toxic form, increases with pH and temperature. In summer, photosynthesis can raise the pH at the end of the day.

— Are nitrates dangerous for fish?

Much less than ammonia and nitrites. Their main problem is that they feed algae; they are limited by plants, size and water renewal.

— Does a UV lamp destroy the filter bacteria?

No, nitrifying bacteria live attached in a biofilm in the filter and on surfaces. UV acts on what circulates in the water, such as suspended algae.

In summary

• Nitrogen enters mainly through food and leaves the fish in the form of ammonia.
• Ammonia toxicity depends on pH and temperature.
• The bacteria transform it into nitrites, which are dangerous, then into nitrates, which feed algae.
• These bacteria need oxygen, KH and water that is not too cold.
• Plants, denitrification and water renewal complete the cycle.

Last updated: October 3, 2026.