The Nitrogen Cycle and How to Cycle a New Reef Tank

By the Coral Compass team · Last reviewed 2026-10-15

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What the nitrogen cycle is

Every fish, coral and bit of uneaten food in an aquarium eventually produces ammonia. Fish excrete it directly through their gills, and bacteria release it as they break down proteins in waste and food. Ammonia is toxic to fish and invertebrates even at low concentrations, so a reef tank needs a living filter that converts it into something safer. That conversion, carried out by bacteria and archaea living on rock, sand and every other surface, is the nitrogen cycle.

The classic summary is three steps:

Ammonia (NH₃/NH₄⁺) is produced by waste and decay.
Nitrite (NO₂^-) is produced when ammonia-oxidizing microbes convert ammonia.
Nitrate (NO₃^-) is produced when nitrite-oxidizing bacteria convert nitrite.

Nitrate is far less toxic than ammonia or nitrite and is removed by water changes, algae, and denitrifying bacteria in low-oxygen zones. In a reef tank a small amount of nitrate is actually useful as a coral nutrient. See our nitrate and phosphate guide.

Who does the work

Older aquarium books name Nitrosomonas and Nitrobacter as the responsible bacteria. Later research found that in aquariums, ammonia oxidation is often dominated by ammonia-oxidizing archaea and other bacteria, nitrite oxidation is mainly done by Nitrospira, and some Nitrospira can perform both steps (called comammox). For the hobbyist the names matter less than three practical facts:

These microbes grow slowly, with doubling times measured in many hours to days, unlike the minutes of many other bacteria.
They live attached to surfaces, mostly in live rock and sand, not floating in the water.
They need oxygen, a source of ammonia, and carbonate (alkalinity) to grow. Nitrification consumes alkalinity.

Ammonia and pH

Test kits report total ammonia, the sum of toxic free ammonia (NH₃) and much less toxic ammonium (NH₄⁺). The balance depends on pH and temperature: the higher the pH, the more of the total is the toxic NH₃ form. At typical reef pH of around 8.1–8.3 and 25 °C, a few percent to around 10% of total ammonia is free ammonia, far more than in acidic freshwater. That is why a reading that would be shrugged off in a freshwater tank can be dangerous in saltwater. In an established reef, total ammonia and nitrite should read zero or effectively undetectable.

Choosing a cycling approach

A new tank has no established microbes. "Cycling" means growing a large enough population to process the waste load you plan to add. There are three main approaches.

1. Fishless cycle with ammonia (recommended)

You add a pure ammonia source to feed the bacteria and track the numbers until the tank can process it quickly. No animals are exposed. This is the most controlled and humane approach and the one most experienced reefers recommend today, especially with dry rock.

2. Fishless cycle with food or a raw shrimp

Decaying food produces ammonia. It works, but the ammonia level is unpredictable, it adds phosphate and organics, and it often triggers stronger algae and diatom outbreaks later.

3. Fish-in cycle

Adding a few hardy fish and letting them supply ammonia was once standard. It exposes the fish to ammonia and nitrite, and is not recommended when fishless options are so easy.

Live rock versus dry rock

Genuine live rock carries microbes, so a tank set up with it may cycle very quickly. The downside is that it may also carry pests such as aiptasia, crabs, mantis shrimp and nuisance algae. Dry rock (mined or manufactured) is pest-free but starts completely sterile and sometimes leaches phosphate. Most new tanks today use dry rock plus bottled bacteria.

Step-by-step fishless cycle

Set up and stabilize. Fill with properly mixed saltwater from RO/DI water at about 1.025–1.026 SG. Run heaters and pumps and get temperature stable around 77–78 °F (25–26 °C). Lights can stay off or low; they are not needed for cycling and only fuel algae.
Add bacteria (optional but helpful). Bottled nitrifying bacteria such as Dr. Tim's One & Only, Fritz TurboStart, Brightwell MicroBacter7 and others can shorten the cycle considerably. Follow the label dose, and do not run UV sterilizers or ozone during this phase.
Dose ammonia to about 2 ppm. Use pure ammonium chloride (for example Dr. Tim's Ammonium Chloride, which is formulated so a set number of drops per gallon gives a known ppm) or unscented household ammonia with no surfactants or fragrances. 2 ppm total ammonia is the target used in most fishless-cycling instructions. Going much higher can slow the cycle.
Test every day or two. Track ammonia, nitrite and nitrate. Expect ammonia to fall first, then nitrite to climb, then nitrite to fall as nitrate rises.
Re-dose ammonia when it falls. Each time ammonia drops near zero, bring it back to about 2 ppm. Keep feeding the bacteria until they are strong.
Watch nitrite. Nitrite often lags and is usually the last thing to clear. Very high nitrite does not harm a tank with no animals, but if it climbs past several ppm and stalls, a partial water change can help.
Watch alkalinity. Nitrification consumes alkalinity. Check it weekly and correct with the dosing calculator if it drops below about 7 dKH. A cycle can stall if alkalinity crashes.
Pass the 24-hour test. The tank is cycled when you can dose 2 ppm of ammonia and both ammonia and nitrite read zero within 24 hours. Many instructions ask for this result two days in a row.
Water change, then stock slowly. Nitrate will be high after a fishless cycle. Do a large water change if you want nitrate near reef levels, then add your first livestock, usually a small clean-up crew and one or two hardy fish, and keep feeding ammonia or food lightly so the bacteria don't starve before the bioload arrives.

How long does it take?

A fishless cycle with dry rock and no bottled bacteria commonly takes four to eight weeks. With a quality bottled bacteria product and ammonium chloride, many tanks pass the 24-hour test within one to three weeks, and some manufacturers claim faster. Tanks set up with mature live rock or rock moved from an established system may barely show a cycle at all. The tank decides, not the calendar. Rely on test results.

The "ugly phase"

Almost every new reef goes through a sequence of nuisance growth after cycling: brown diatoms on sand and glass, then often green hair algae, cyanobacteria or even dinoflagellates. This is normal. New tanks have unstable nutrient levels and few competitors. A clean-up crew, patience, moderate feeding, stable lighting and regular maintenance usually get the tank through it. See our pests and nuisance algae guide for what to do if cyano or dinos settle in.

Common mistakes

Trusting the calendar. "Four weeks" means nothing without a passing ammonia test.
Adding a full load at once. Even a cycled tank's bacteria population is sized to the load it was fed. Add livestock gradually over weeks and months.
Using scented ammonia. Fragrances and surfactants can harm the tank. Use pure ammonium chloride or plain ammonia.
Letting alkalinity fall. A stalled cycle is often an alkalinity problem.
Misreading test kits. Some ammonia kits read falsely high in saltwater or are thrown off by certain water conditioners. If readings don't make sense, try a second kit designed for saltwater.
Killing the bacteria. Some medications, especially many antibiotics, can damage nitrifiers. Treat fish in a separate quarantine tank.

Mini-cycles in established tanks

An established tank can briefly show ammonia or nitrite after a large die-off, a dead fish hidden in the rock, overfeeding, a power outage that kills bacteria in a canister or sump, or adding a large group of fish at once. If ammonia appears, reduce feeding, do a water change, find the source, and consider bottled bacteria. Products that bind or detoxify ammonia (such as Seachem Prime) can protect livestock temporarily while the cause is fixed.

Summary

The nitrogen cycle turns toxic ammonia into nitrite and then into much safer nitrate, carried out by slow-growing microbes living on surfaces. Cycle fishless with ammonia to about 2 ppm, use bottled bacteria if you like, keep alkalinity up, and wait until 2 ppm of ammonia disappears within 24 hours. Then stock slowly and expect an ugly phase before the tank settles.

Frequently asked questions

How do I know my saltwater tank is cycled?

Dose ammonia to about 2 ppm. If both ammonia and nitrite read zero within 24 hours, ideally on two consecutive days, the tank is cycled for its first livestock.

How long does it take to cycle a reef tank?

Typically four to eight weeks with dry rock and no bacteria additive, and often one to three weeks with a quality bottled bacteria product. Rely on test results, not the calendar.

Do I need lights on while cycling?

No. Nitrifying bacteria do not need light. Keeping lights off or low during the cycle reduces early algae.

Why is my nitrite stuck high?

Nitrite oxidizers often lag. Check that alkalinity is not depleted, avoid overdosing ammonia, and consider a partial water change if nitrite is very high and not dropping.

Is nitrate bad after cycling?

It is far less toxic than ammonia or nitrite. Reduce it with a water change before adding corals, but a reef tank should keep a small, detectable amount of nitrate.

Open the free dosing calculator

More reef science guides

Ranges are common hobby targets compiled from reef chemistry literature (including Randy Holmes-Farley's articles), hobby consensus and manufacturer documentation. They're not rules. Last reviewed 2026-10-15.