Cycling an aquarium: the nitrogen cycle explained

A new aquarium looks completely ready: the water is clear, the filter is humming, the plants are in. That very look is the biggest trap for a beginner – clear water is not the same as safe water. Before fish move in, an invisible colony of bacteria has to grow inside the filter and break down toxic waste as it appears. This process is called the nitrogen cycle, and it takes weeks, not days.

What the nitrogen cycle actually is

Fish release ammonia as they metabolise protein, and decaying uneaten food and dying plant matter add more. In a closed aquarium the ammonia has nowhere to disperse, so it builds up. The solution is biological: two groups of bacteria colonise the filter media and every other surface. The first convert ammonia into nitrite, the second convert nitrite into nitrate.

Nitrate is the last link in the chain and far less dangerous to fish – we remove it with regular water changes, and plants use up part of it. The key point is that the first two links are not harmless: until the bacterial colonies are large enough, ammonia and nitrite accumulate to levels that damage or kill fish.

Why ammonia and nitrite are so dangerous

Ammonia exists in water in two forms – un-ionised ammonia (NH₃) and the ammonium ion (NH₄⁺). It is mainly the first form that is toxic. A concentration of around 0.05 mg/L of un-ionised ammonia is already enough to cause changes in gill tissue, and roughly 2 mg/L is lethal for many species.

One important detail beginners often miss: the toxic fraction rises with higher pH and higher temperature, and pH has more influence than temperature. The same measured total ammonia is therefore considerably more dangerous in warm, alkaline water than in cooler, slightly acidic water.

Nitrite works differently: it passes from the water into the blood, where it converts haemoglobin into methaemoglobin, which cannot carry oxygen. The condition is known as "brown blood disease" because the gills take on a chocolate-brown shade. A fish in this state suffocates even though there is plenty of oxygen in the water.

Fishless cycling: the safest method

Instead of putting live fish under strain, you add a source of ammonia yourself and wait for the bacteria to grow. For this method veterinary sources suggest raising ammonia to a few milligrams per litre (in practice usually around 1–5 mg/L) and maintaining it until the cycle completes.

Step by step:

• Fill the tank, start the filter and heater, and plant it out.
• Add a source of ammonia (pure ammonia with no additives, or a small amount of food left to decay).
• Every few days measure ammonia, nitrite and nitrate with liquid test kits.
• Ammonia rises first, then starts to fall as nitrite rises, and finally nitrate appears.
• The cycle is finished when ammonia and nitrite both drop to zero within a day and nitrate is measurable.

Do a large water change before stocking to bring down the accumulated nitrate. Add your first fish in small groups – the bacterial colony has to adapt to every increase in load.

How long it takes

Patience really is part of the procedure here. A biofilter in a tropical tank can take up to eight weeks to establish. You can speed things up by transferring filter sponge, some substrate or decor from an established aquarium – the bacteria come with them. It is well worth asking a fellow aquarist or a local shop for a piece of mature filter media.

Once the tank is cycled: what to keep measuring

In an established aquarium, ammonia and nitrite should stay permanently at zero. Nitrate builds up slowly; for freshwater tanks a figure of around 20 mg/L is quoted as a sensible upper limit, maintained through regular partial water changes.

Watch out for actions that can crash the cycle: rinsing the filter sponge thoroughly under tap water (chlorine kills the bacteria), replacing all filter media at once, treating the tank with antibiotics, and overfeeding. Rinse filter sponge only in water siphoned out of the aquarium, and never replace all the media at the same time.

First fish: choose hardy species

Even in a properly cycled tank it makes sense to start with species that tolerate minor fluctuations. Among the most suitable for beginners are the zebra danio and the guppy; we have collected a wider selection in 10 best aquarium fish for beginners.

If you have not set the tank up yet, start with the basics – equipment, size and setup are covered in our guide How to set up your first aquarium.

If your fish show signs of distress despite a correct procedure – rapid breathing, hanging at the surface, listlessness – test the water first and do a partial water change; for unclear or persistent problems, consult a veterinarian who treats aquarium animals.