Aquarium nitrogen cycle explained, with week-by-week readings

The aquarium nitrogen cycle is the process in which microbes living on your filter media and tank surfaces turn toxic ammonia from fish waste into nitrite, and then into much less harmful nitrate, which you remove with water changes. A new tank usually needs 4 to 8 weeks to grow these microbes, or a few days to 2 weeks with filter media from a healthy established tank. In a fishless cycle, it is complete when a 2 ppm dose of ammonia reads 0 ppm ammonia and 0 ppm nitrite 24 hours later while nitrate keeps rising.

Every fish tank runs on the same chain. Fish make ammonia, microbes turn it into nitrite, other microbes turn that into nitrate, and you take the nitrate out with water changes. Build that chain before you add fish and the water stays safe.

Ammonia, nitrite and nitrate at a glance

All three show up on a standard freshwater test kit. Readings are in ppm, which is the same as mg/L.

Compound	Where it comes from	How harmful it is	Target reading
Ammonia (NH₃ / NH₄⁺)	Fish gills and waste, uneaten food, dead fish, rotting plants, some tap water	Highly toxic. The free form (NH₃) is far more toxic than ammonium (NH₄⁺), and its share rises with pH and temperature	0 ppm
Nitrite (NO₂⁻)	Made from ammonia by ammonia oxidizers	Toxic. Sensitive fish can be harmed at levels as low as 0.1 ppm. It cuts the blood’s ability to carry oxygen	0 ppm
Nitrate (NO₃⁻)	Made from nitrite by nitrite oxidizers	Much less toxic, but it can cause harm when it builds up for months	Under 40 ppm, ideally 20 ppm or less

Here is the chain in order:

Ammonia goes in. Fish release most of their nitrogen waste as ammonia, straight from their gills.
Ammonia becomes nitrite. Ammonia-oxidizing microbes living on filter media and other surfaces use oxygen to convert it.
Nitrite becomes nitrate. Nitrite-oxidizing bacteria convert nitrite into nitrate.
Nitrate comes out. In a normal tank almost nothing breaks nitrate down, so it builds up until you remove it with water changes. Plants take up some nitrogen as well.

Nitrification uses up oxygen and carbonate hardness (KH) as it runs. That is why a cycling tank needs good water movement, and why pH slowly drifts down in a tank that rarely gets water changes.

Why the nitrogen cycle matters

A brand-new filter has almost no nitrifying microbes. Fish start making ammonia on day one, and ammonia, then nitrite, builds up faster than the colony can grow. This is new tank syndrome, and it usually shows up in the first few weeks. Fish look fine for a few days, then gasp at the surface, clamp their fins, hide or die. If your fish already show these signs, test ammonia and nitrite and change water straight away, using a dechlorinator as its label directs and water at the same temperature. If they don’t recover once the water tests clean, contact an aquatic vet.

The cycle still matters long after setup. The colony grows to match the waste it gets, and no bigger. A sudden jump in waste (a big batch of new fish, a dead fish left in the tank, heavy overfeeding) or a loss of microbes (filter media cleaned in tap water, some medications) brings ammonia or nitrite back. Hobbyists call this a mini-cycle.

pH changes how dangerous ammonia is

Test kits measure total ammonia. The share in the toxic free form depends on pH and temperature, and across normal aquarium pH it rises roughly tenfold for each 1.0 step up in pH. At 77 °F (25 °C), a 1 ppm reading contains about:

pH	Share in the free (toxic) form	Free ammonia in a 1 ppm reading
6.5	0.2%	0.002 ppm
7.0	0.6%	0.006 ppm
7.5	1.8%	0.018 ppm
8.0	5.4%	0.054 ppm
8.5	15%	0.15 ppm

These shares come from the standard equation behind the UF/IFAS ammonia table. UF/IFAS warns that free ammonia above 0.05 ppm can damage fish tissue, so at pH 8 and above a 1 ppm reading is already past that line, while the same reading at pH 6.5 buys a little time. Warmer water raises the toxic share further. Treat any reading above zero as a problem either way. The ammonia guide has the emergency steps.

Who does the work: bacteria, archaea and comammox

Older articles and many bottle labels name two bacteria: Nitrosomonas for the ammonia step and Nitrobacter for the nitrite step. Studies of real aquarium filters disagree.

Step	The old textbook answer	What studies of freshwater aquarium filters found
Ammonia → nitrite	Nitrosomonas (ammonia-oxidizing bacteria, or AOB)	Ammonia-oxidizing archaea (AOA) and comammox Nitrospira usually dominate. AOB are scarce except where ammonia runs high, such as during setup
Nitrite → nitrate	Nitrobacter	Nitrospira bacteria, not Nitrobacter
Ammonia → nitrate in one cell	Not known before 2015	Comammox (“complete ammonia oxidation”) Nitrospira, first described in 2015, do both steps alone

The key studies, in order:

1998: Hovanec and colleagues linked nitrite oxidation in freshwater aquaria to Nitrospira-like bacteria. They found no Nitrobacter, even in tanks dosed with a product that contained it.
2011: Sauder and colleagues found archaea outnumbered ammonia-oxidizing bacteria in 23 of 27 freshwater filters, with the bacteria making up a bigger share where ammonia was higher.
2024: McKnight and Neufeld found comammox Nitrospira in all 38 freshwater filters they sampled from homes and stores, and as the main ammonia oxidizer in 30 of them. Archaea led in most of the rest, and ammonia-oxidizing bacteria were scarce.
2025: The same group followed three new home aquariums with fish for 12 weeks. Ammonia and nitrite cleared by week 3 in two tanks and by week 8 in the third. One tank had an early AOB phase, but comammox Nitrospira dominated all three filters from week 6 onward.

What this means for you: trust your test kit, not the label. Whatever a bottle names, the proof is ammonia and nitrite falling to 0 while nitrate rises. The microbes that dominate mature tanks also appear suited to low, steady ammonia. They handle a steady load well but need days to weeks to catch up with a sudden big one, so add fish in batches.

Week by week: typical readings during a cycle

The chart and table show a typical fishless cycle: ammonia started at 2 ppm and fed about 1 ppm at a time during the nitrite phase, water at about 78 °F (26 °C), pH between 7 and 8, and no bottled bacteria. This is a composite of published timelines, not a log from one tank. Dr Tim’s Aquatics puts an unassisted fishless cycle at 30 to 45 days, the Merck Veterinary Manual says a new biofilter usually takes about 6 weeks, and UF/IFAS allows 6 to 8. Seeded media can shrink it to a week or two, and cold, soft or acidic water can stretch it past eight weeks.

Typical fishless cycle started at 2 ppm ammonia. Each line is scaled to its own peak (solid: ammonia, dashed: nitrite, dotted: nitrate). The real numbers are in the table below.

Week	Ammonia	Nitrite	Nitrate	What is happening	What to do
0 (day 1)	2 ppm (dosed)	0	0*	Almost no nitrifiers yet	Dose to 2 ppm. Test every 2–3 days
1	1–2 ppm, slowly falling	0–0.25 ppm	0*	Ammonia oxidizers start to multiply	Don’t add ammonia until it drops below 0.5 ppm
2	0.25–1 ppm	0.5–2 ppm	0–5 ppm	Nitrite appears and ammonia drops faster	Test every day or two. Once nitrite shows, add about 1 ppm (half the first dose) each time ammonia falls below 0.5 ppm
3	0 within 1–2 days	2–5 ppm, often the top of the test chart (peak)	5–20 ppm	Nitrite spike. Nitrite oxidizers lag behind	Add about 1 ppm each time ammonia is gone. If nitrite reads 5 ppm or more, stop dosing and change 30–50%
4	0 within 24 h	1–2 ppm, falling	20–40 ppm	Nitrite oxidizers catch up	Keep adding about 1 ppm each time ammonia is gone
5	0 within 24 h	0–0.5 ppm	40 ppm and up	Nearly finished	Once nitrite is falling steadily, go back to a full 2 ppm dose and start the 24-hour test
6	0 within 24 h	0 within 24 h	40–100 ppm or more	Cycled	Pass the 24-hour test twice, then do a big water change

*Plus whatever nitrate is already in your tap water. Many nitrate tests also react to nitrite, so mid-cycle nitrate readings can look higher than they are.

Nitrate keeps climbing because the nitrogen doesn’t leave the tank. It only changes form. On most hobby kits, which report each compound as the whole ion, 1 ppm of ammonia becomes up to about 2.7 ppm of nitrite and then up to about 3.6 ppm of nitrate. That is why the nitrite peak can read higher than the ammonia you dosed. It also makes nitrate a useful cross-check. If ammonia disappears but nitrate never rises, something else is taking the ammonia (often plants) or one of your tests is off.

A fish-in cycle follows the same pattern with lower peaks, because you hold ammonia and nitrite down with water changes. The full procedure for both methods is in how to cycle a fish tank.

How to tell the cycle is complete

For a fishless cycle, use the 24-hour test:

Work out how much water the tank really holds with the aquarium volume calculator. Substrate and decor mean it holds less than the label says. Using plain ammonia with no scent or soap, add a little at a time until the test reads 2 ppm.
Wait 24 hours, then test ammonia, nitrite and nitrate.
You pass if ammonia is 0, nitrite is 0 and nitrate is higher than before the dose.
Dose again and repeat the next day. Two passes in a row means it’s ready.
Do one or two large water changes with dechlorinated, temperature-matched water to bring nitrate to 20 ppm or less. If your tap water has no nitrate, going from 80 ppm to 20 ppm takes about a 75% change.
Add fish within a day or two. If they will be longer, keep dosing ammonia every day or two, because the colony shrinks without food.
Add fish in stages. The colony is sized to the ammonia you fed it, so test ammonia and nitrite every day or two for a week after each new batch. The stocking calculator helps you plan the final stock.

For a fish-in cycle, the tank is cycled when ammonia and nitrite read 0 on every test for about a week of normal feeding with no water changes in between, and nitrate is climbing.

Reading your test results

Ammonia	Nitrite	Nitrate	What it usually means
Above 0	0	0	Very start. Ammonia oxidizers are still scarce
Falling	Rising	Low	Halfway. The first colony works and the second is lagging
0	Above 0	Rising	Last stretch. Wait for the nitrite oxidizers
0	0	Rising	Cycled for the current load, if it holds for several days
Above 0	Above 0	High, in an older tank	Mini-cycle. The colony was damaged or overloaded

Log each reading with the date, for example in My tanks. A trend over several days tells you far more than one test.

What speeds up or stalls the cycle

Factor	Helps	Slows or stalls
Temperature	Tropical temperatures, about 76–82 °F (24–28 °C)	Cold water. FAO aquaponics guidance says the bacteria work more slowly below about 63 °F (17 °C)
pH and KH	pH 7 to 8, and KH of at least 3 dKH (about 54 ppm), ideally 5–6 dKH (about 100 ppm)	pH below 7. Dr Tim’s Aquatics says cycling stalls there. UF/IFAS says common nitrifying bacteria don’t work well below 20 ppm alkalinity (about 1 dKH)
Oxygen	Filter running day and night, rippling surface	Filter switched off for hours, stagnant water
Ammonia dose	About 2 ppm to start, then about 1 ppm at a time while nitrite is high	Ammonia above 5 ppm, or nitrite at 5 ppm or more for days
Seeding	Media or gravel from a healthy established tank, live bottled bacteria	Only brand-new media (slower, but not harmful)
Water and chemicals	Dechlorinated tap water	Chlorine or chloramine, some medications (especially antibiotics), ammonia-removing products during a fishless cycle

Only borrow media from a tank whose fish are healthy, because media can carry disease as well as bacteria. Live plants take up some ammonia and help a little, but they don’t replace a cycled filter. If you must treat sick fish in a new tank, follow the product label, test ammonia and nitrite daily, and ask an aquatic vet about treatments that are gentler on the filter. If your test kit reports KH or alkalinity in ppm, the unit converter turns it into dKH (1 dKH is about 17.8 ppm).

Common mistakes that crash or fake a cycle

Cleaning filter media under the tap. Chlorine or chloramine kills the colony. Swish media in old tank water instead. See how to clean a fish tank.
Replacing all the filter media at once. Change sponges or cartridges in stages, or keep part of the old media running.
Testing ammonia only. Ammonia at 0 with nitrite at 2 ppm is a tank that is only half done.
Overdosing ammonia. More ammonia does not grow the colony faster. Start at about 2 ppm, never go above 5 ppm, and drop to about 1 ppm doses once nitrite appears, or the nitrite peak can climb high enough to slow the nitrite oxidizers.
Letting nitrate run away. A cycled tank still needs regular water changes. See water changes: how often and how much.

Gear mentioned in this guide

Liquid test kit (ammonia, nitrite, nitrate, pH) (opens Amazon in a new tab)Liquid kits are more accurate than strips. The API Freshwater Master Test Kit is the common choice. How to choose
Bottled nitrifying bacteria (opens Amazon in a new tab)Can help a new tank cycle. Still test the water before adding fish. How to choose
Pure ammonia for a fishless cycle (opens Amazon in a new tab)Use ammonia with no soap or scent. Dose to about 2 ppm. How to choose

Product links go to Amazon search results. As an Amazon Associate we earn from qualifying purchases, at no extra cost to you. Disclosure.

Frequently asked questions

How long does the nitrogen cycle take in a new aquarium?

Without help, most tanks take about 4 to 8 weeks, and UF/IFAS allows 6 to 8 weeks for a new biofilter. Filter media from a healthy established tank can cut that to a few days or 2 weeks, while live bottled bacteria vary from days to several weeks. Only your test results tell you it is finished.

Can I add fish while the tank is cycling?

You can (this is called a fish-in cycle), but keep the stock small, test ammonia and nitrite every day, and change water the same day either shows any reading (0.25 ppm on most kits), because nitrite can harm fish from about 0.1 ppm. A fishless cycle, where you dose ammonia instead of keeping fish, builds the colony without putting any animals at risk.

Do water changes remove the beneficial bacteria?

No. Most nitrifying microbes live attached to filter media, gravel and decor rather than floating in the water, so a dechlorinated water change does not undo the cycle. Rinsing filter media in chlorinated tap water or replacing all of it at once can.

Why is my nitrite high and not going down?

Nitrite oxidizers can only multiply once there is nitrite to feed on, so they lag behind, and a nitrite peak lasting one to three weeks is normal. If it drags on, check that pH is above 7 and KH is not near zero, and stop adding ammonia while nitrite reads 5 ppm or more. A 30 to 50% water change, then smaller doses of about 1 ppm, often gets it moving again.

Is 0 ammonia, 0 nitrite and 0 nitrate a cycled tank?

Not on its own. A working cycle produces nitrate, so all zeros usually means nothing is feeding the bacteria, plants are taking up the nitrogen, or a test is out of date. In a tank with no fish, dose ammonia to 2 ppm and check that it turns into nitrate within 24 hours; never add ammonia to a tank that has fish in it.