Cycling a new aquaponics system

Cycling is the period when a new aquaponics system grows the bacteria that turn fish waste into plant food. Until those bacteria are established, the ammonia fish produce builds up in the water, and in a few gallons it reaches harmful levels within days. Cycling first, with no fish in the tank, protects the fish and gives you a system that can handle them from the day they arrive. The chemistry behind each stage is in our guide to the nitrogen cycle, and this page is the procedure.

What you need before you start

Most of this you'll already have if the system is built.

The system running with its pump, grow bed, and media in place, filled with dechlorinated water.
An ammonia source. Use plain household ammonia with no scent or surfactants (it shouldn't foam when you shake the bottle), or ammonium chloride sold for fishless cycling.
A liquid test kit covering ammonia, nitrite, nitrate, and pH. Strips are less precise at the low readings that matter here.
A heater set to about 25 to 28°C (77 to 82°F) if the room is cool, since warm water cycles faster.
Optionally, seed material such as a used sponge or a handful of media from a healthy, established aquarium.

Fishless cycling, stage by stage

Run the system for a day to make sure the pump and the fill and drain both work. Then add ammonia a little at a time until the test reads about 2 ppm. With household ammonia in a small tank that can be only a handful of drops, so add it slowly and test between doses. From then on, test every day or two and write the results down, because the pattern over time tells you more than any single reading.

Ammonia only

For the first week or two, ammonia holds near the level you dosed while nitrite stays at zero, and it can look as if nothing is happening. The ammonia-oxidizing bacteria are multiplying from very small numbers during this time. If ammonia falls below about 1 ppm, top it back up to 2 ppm.

Nitrite appears

Once the first group takes hold, ammonia starts falling and nitrite starts rising. Keep dosing back to 2 ppm whenever ammonia drops toward zero, so both groups of bacteria keep growing. If nitrite reads off the top of the kit's color chart for more than a few days, a water change of about 30% brings it back into range, because very high nitrite can slow the second group down.

Nitrite falls and nitrate rises

In the last stage nitrite drops as the nitrite-oxidizing bacteria catch up, and nitrate climbs. This often happens quite suddenly after a week or more of high nitrite readings. Keep dosing ammonia daily through this stage so the bacteria stay fed.

How to tell it's finished

The system is cycled when it can take a 2 ppm dose of ammonia down to zero within 24 hours, with nitrite also reading zero. Run that test on two days in a row to be sure. Nitrate will be high by then, so do a large water change, 50% or more, with dechlorinated water before adding fish.

Add the first fish within a day or two so the bacteria don't go hungry, and if there's a delay, keep dosing a small amount of ammonia each day. Stock in stages, starting with about half the planned fish, as our guide to feeding and stocking describes.

How long does cycling take?

From a cold start, expect roughly three to six weeks, and longer in cool water. Seeding with a sponge or media from a healthy established aquarium can cut that substantially, because you're transplanting a working population of bacteria and skipping the slow start. Bottled bacteria products shorten cycling for many people too, though results vary with the product and how it was stored. Whichever route you take, the 24-hour test above is the way to know the job is done.

When cycling stalls

A cycle that seems stuck for more than a week or two usually has one of a handful of causes, and each has a simple fix.

Low pH. Nitrification makes the water more acidic, and below about 6.5 the bacteria slow noticeably. Test pH and KH and raise them gently if needed, as our water testing guide explains.
Cold water. Below about 20°C (68°F) everything takes longer. A heater helps.
Too much ammonia. Doses far above 2 ppm can slow the bacteria. Do a partial water change and dose back to 2 ppm.
Chlorine or chloramine. Topping off with untreated tap water can kill bacteria, so treat every top-off with dechlorinator.

Cycling with fish in the tank

Some people cycle with a few hardy fish in the tank. It can work, but it's harder on the fish and more work for you, because ammonia and nitrite have to be held below about 0.5 ppm the whole time with daily testing and frequent partial water changes for several weeks. If you go this way, start with one or two fish, feed very lightly, and keep a container of dechlorinated water ready. In a small system fishless cycling is easier to control, which is why we recommend it.

Planting during cycling

You can plant while the system cycles. Hardy herbs and leafy greens tolerate the ammonia levels used in fishless cycling, and their roots add surface for bacteria. Expect slow growth and some yellowing until nitrate builds up, and hold off on treating it as a deficiency until the system has been stocked for a few weeks. Our article on starting a desktop aquaponics system covers the rest of the setup sequence, including tank size and grow media.