Cycling Stalled: Why Ammonia or Nitrite Will Not Drop

A cycle stalls when nitrifying bacteria are starved of alkalinity, kept too cool, poisoned by chlorine or treatments, or overloaded. Test each cause, correct it and reseed.

A cycle that "stalls" usually has not failed: the nitrifying bacteria are growing slowly or have been set back. The most common reasons are pH and alkalinity that have fallen too low, water that is too cool, residual chlorine or chloramine, disease treatments added to the tank, and too much ammonia. Each can be confirmed with a simple test and corrected before the biofilter is reseeded.

What the symptom looks like

In a normal start-up, total ammonia rises to a peak and falls; after a lag, nitrite rises, peaks and falls; nitrate then accumulates (SRAC Publication 4502). The MSD Veterinary Manual describes a biofilter as mature once ammonia and nitrite have peaked and dropped and nitrate is rising, and gives roughly 6 weeks for a new biofilter to establish fully. SRAC Publication 452 states that activating a new biofilter takes at least 1 month. A stall is when ammonia or nitrite stays on a plateau for well beyond that, with no rise in nitrate.

Timelines vary widely. In a 12-week study of three new home aquariums, measurable nitrification began only from about week 6–7, and Wikipedia notes reports of cycling taking up to six months. A plateau at three or four weeks is therefore not proof of a problem; a plateau combined with one of the causes below is.

Likely causes and the test that confirms each

Low pH and depleted alkalinity (KH). Nitrification produces acid and consumes alkalinity, so pH drifts down as the cycle progresses (SRAC 451, 452). SRAC 452 gives 7–8 as the optimum pH for biofilter bacteria and states that below pH 6 they are inhibited; SRAC 451 notes that pH below 7.0 already reduces their activity. Test: pH and KH (alkalinity) on the same day. A falling KH with a falling pH points here.
Water too cool. Nitrification is a biological reaction and runs faster when warm; the example start-up in SRAC 4502 was fast because it ran at 28 °C (about 83 °F). Test: a thermometer reading compared with the temperature the tank will run at.
Residual chlorine or chloramine. SRAC 4502 requires system water to be free of residual chlorine before seeding, and notes that chlorine disinfection kills nitrifying bacteria. Chloramine persists much longer than chlorine when water stands (Wikipedia). Test: a chlorine test on the tap water, and a check of whether every top-up was treated with a dechlorinator that neutralises chloramine.
Disease treatments. SRAC 452 lists formalin, copper sulfate, potassium permanganate and certain antibiotics as inhibiting biofilter bacteria, and notes that even a sudden change in salt concentration reduces biofilter efficiency. Test: a log of anything added to the tank since start-up.
Too much ammonia. Wikipedia notes that too high an ammonium concentration can kill nitrifiers. For a fishless start, SRAC 4502 targets 3–5 mg/L total ammonia. Test: total ammonia well above that range, with no downward trend.
Media and flow. SRAC 4502 notes that brand-new, smooth media can be slow to colonise, and that heavy agitation in moving-bed filters can scrape off attaching bacteria. Test: new media only, or a very turbulent filter bed.

Immediate safe actions

If fish are present, protect them first: test ammonia and nitrite daily, do water changes to keep them down, and stop or sharply reduce feeding until the problem is corrected (MSD Veterinary Manual). The separate guide Cycling a Tank With Fish Already In It covers this in detail.
Restore alkalinity and pH gradually. SRAC 4502 suggests raising alkalinity to about 150 mg/L as CaCO3 for a fishless start-up, with better nitrite-oxidiser establishment at about 200–250 mg/L, using sodium bicarbonate (baking soda). Its rule of thumb, given for a start-up before any animals are stocked: 53 g of sodium bicarbonate per 3,785 L (1,000 US gal) raises alkalinity by about 10 mg/L. With alkalinity at that level, it notes, pH is usually not a problem, and 6.8–7.2 is a good range.
Bring the temperature close to the planned running temperature. SRAC 4502 allows raising it 2–3 °C above that to speed growth, but no more, to avoid a die-off when it is lowered again.
Treat all new water for chlorine and chloramine, and keep medications out of the cycling tank where possible.
If ammonia is far above 3–5 mg/L in a fishless tank, dilute it with treated water changes and dose less in future.

How to restart a stalled cycle

Once the cause is removed, the bacteria need a source of ammonia and time. SRAC 4502 describes the sequence: correct water chemistry first, add an ammonia source to 3–5 mg/L total ammonia, introduce bacteria, then test ammonia, nitrite, pH, temperature and alkalinity at the same time each day and graph them. The most effective seed, according to SRAC 4502, is media moved from an established system kept under similar conditions; any transfer of water, media or animals can also bring in pathogens. Prepared cultures of nitrifying bacteria are not essential but can shorten start-up. Watch for the nitrite curve to turn down: its peak marks the point at which nitrite oxidisers consume more than is produced.

Several microbial groups do the work in home aquariums, not only the classic ammonia- and nitrite-oxidising bacteria: the 12-week home-aquarium study found complete ammonia-oxidising (comammox) Nitrospira dominating biofilters from week 6 onward. The guide Nitrification Microbiology in RAS Biofilters describes these organisms.

When it is disease

Fish piping at the surface with chocolate-brown gills during a nitrite plateau suggest nitrite poisoning (brown blood disease); see Nitrite Toxicity and Chloride Protection: Brown Blood Disease Explained. Lethargy, poor appetite, spinning or convulsions during an ammonia plateau point to ammonia toxicity (MSD Veterinary Manual). Lesions, white spots or frayed fins are signs of an infection that the stress of a stalled cycle may have triggered; use the disease article that matches the signs.