How the nitrogen cycle works in a small aquaponics system

A desktop aquaponics tank runs on the same chemistry as a backyard system a hundred times its size. Fish release ammonia, two groups of bacteria convert it to nitrate, and the plants take that nitrate up as fertilizer. When those three stay in step, the water stays safe for the fish without the routine water changes a plain aquarium needs, and a small system has far less room for them to drift apart.

If you're setting up a system right now, the step-by-step process is in our guide to cycling a new system. This page explains the chemistry behind those steps, which helps when a test result doesn't look the way you expected.

Where the ammonia comes from

Fish excrete most of their nitrogen waste as ammonia, released straight through the gills, and a smaller share comes from droppings and uneaten food as they break down. The amount tracks closely with feeding. More food, and especially more protein, means more ammonia, which is why the feeding rate is the real throttle on a small system and why our guide to feeding and stocking matters as much as any piece of equipment.

Home test kits report this as total ammonia, which combines two forms. Ammonium (NH4+) is relatively harmless, while free ammonia (NH3) is the toxic one, and the balance between them shifts with pH and temperature. At 25°C (77°F) and pH 7.0, well under 1% of the total is in the toxic form. At pH 8.0 it's roughly ten times that. The same 1 ppm reading is far more dangerous in hard, alkaline water than in a system running near neutral, which is one reason aquaponics growers keep pH at or a little below 7.

The two bacterial steps

The first step belongs to ammonia-oxidizing microbes, usually described as Nitrosomonas bacteria, which convert ammonia into nitrite. Nitrite is toxic too. It interferes with the way fish blood carries oxygen, so fish exposed to it can look like they're struggling for air even in well-aerated water.

A second group, the nitrite-oxidizing bacteria, converts nitrite into nitrate. Older aquarium books credit Nitrobacter with this step, but a 1998 study of freshwater aquarium filters by Timothy Hovanec and colleagues found Nitrospira-like bacteria doing most of the work. For a hobbyist the name matters less than the timing. The second group can't build up until the first is producing nitrite for it to use, which is why nitrite rises late during cycling and is the last reading to fall to zero.

Both groups grow slowly. Under good conditions they take many hours to double, where common bacteria can double in well under an hour, so a population large enough to handle a full load of fish takes weeks to build. No product or trick changes that biology much, though seeding a new system with established media gives it a head start.

Where the bacteria live

Nitrifying bacteria live as a thin film on surfaces, with very few floating free in the water. In an aquaponics system that means the grow bed media, the walls of the tank and pipes, the sponge on the pump intake, and the plant roots themselves. Because of that, changing water doesn't remove them, but rinsing media or sponges under chlorinated tap water can kill a large share of them. When a sponge needs cleaning, squeeze it out in a bucket of tank water.

Surface area sets the ceiling on how many bacteria a system can hold, and so on how much ammonia it can process. That's why the choice of grow bed media matters for filtration as well as for plants, which our guide to mechanical and biological filtration covers in detail.

What the bacteria need

Nitrifying bacteria are aerobic. They need dissolved oxygen and slow down sharply in stagnant water, so the flood-and-drain cycle or steady flow through the grow bed is doing filtration work as much as watering. A grow bed corner that never drains, or a pump that stops for a day, shows up in the ammonia reading soon after.

Temperature sets their pace. FAO's manual on small-scale aquaponic food production gives 17 to 34°C (63 to 93°F) as the ideal range for nitrifying bacteria, notes that productivity drops below 17°C, and says it can fall by half or more below 10°C. A tank in a cool room in winter can show ammonia it never showed in summer at the same feeding rate.

pH matters as well. The bacteria work best around 7 to 8, most vegetables prefer slightly acidic water, and fish sit somewhere between. The FAO manual recommends a compromise of 6 to 7. Many small-system growers keep to the top of that range, around 6.8 to 7.0, because nitrification slows as pH falls and gets very slow below about 6.

Why pH falls over time

Nitrification produces acid. As the bacteria convert ammonia, they use up the water's carbonate buffer, which test kits report as KH or alkalinity. With hard tap water this can go unnoticed for months. Once the buffer is spent, pH can drop quickly, and a lower pH slows the very bacteria that caused the drop.

That downward drift is normal in a working aquaponics system. Most growers correct it with small additions of a carbonate or hydroxide buffer, often alternating potassium and calcium compounds because plants in aquaponics tend to run short of both. The details, and the leaf symptoms to watch for, are in our guide to plant nutrient deficiencies. Testing pH and KH weekly lets you catch the slide before it reaches the fish.

Where the nitrate goes

Nitrate is the end of the bacterial chain and the start of the plant side. It's far less toxic than ammonia or nitrite. The FAO manual allows 5 to 150 ppm in food-fish systems, although small aquarium fish and shrimp do better toward the low end of that range. In a balanced desktop system the plants take nitrate up about as fast as it's produced, so readings hold steady somewhere around 5 to 40 ppm.

Steadily rising nitrate means the fish and feed are outpacing the plants, and our article on the best plants for filtration covers which species pull the most. A reading stuck at zero, with healthy fish and pale plants, usually means the grow bed could support a little more feed.

Reading the cycle on a test kit

Because each step depends on the one before it, the three readings together tell you where a problem sits. Ammonia above zero means the first group can't keep up, whether from too much feed, too few bacteria, cold water, or low pH. Nitrite with ammonia near zero means the second group is lagging, which is common in the first weeks after stocking. Ammonia and nitrite both at zero with some nitrate present means the whole chain is working.

Our guide to water testing covers how to get reliable numbers from a home kit and what to do about each one. To see the bacterial stage alongside the mechanical and plant stages, read the article on how aquaponics filtration works.