Growing fish and plants together lets you produce more food in less space while using fewer resources than conventional growing methods. Once your system is up and running, your main jobs are checking pH, nitrate levels, water temperature, and a handful of other numbers, plus feeding your fish on a normal schedule. From there, the system largely takes care of itself: fish waste feeds beneficial bacteria, which turn ammonia into nitrite and then into nitrate that your plants absorb as food. Because you’re able to control the growing environment so closely, crops typically develop quicker than they would in soil. Getting to that point, though, means setting the system up correctly first, and that starts with cycling it properly and checking on it consistently.

What Does Cycling Actually Do?

Cycling is the process of building up the bacteria that turn ammonia into nitrite, then into nitrate — the form your plants can actually use. Fish waste is the raw material bacteria feed on to create this plant nutrition. The catch is that if you drop fish and plants into a brand-new system right away, none of those bacteria exist yet. Cycling is simply the waiting period you go through before launch, so the right bacterial colonies are already established by the time fish and plants move in together.

Why Skipping This Step Is a Bad Idea

The whole point of cycling is to grow and multiply the bacteria colony responsible for turning fish waste into usable nitrate. It’s a mandatory early step for any new system — without it, your plants won’t have the nutrients they need to thrive.

Two Ways to Cycle a System

You’ve got two main paths: cycling with live fish in the tank, or cycling without any fish at all. Neither is objectively better — pick whichever fits your comfort level. Either way, expect the process to run roughly four to six weeks. Keep your water between 68°F and 86°F (20°C to 30°C) throughout — fall outside that band and the bacteria multiply more slowly, which drags the timeline out further. The bacteria strains you’re relying on, Nitrosomonas and Nitrobacter, reproduce best in water with a pH between 7 and 8; outside that window, expect slower colony growth. One rule to remember: never use lime to raise your pH, since it will kill off the bacteria you’re trying to grow.

Cycling With Fish Already in the Tank

Start by building the physical system: the fish tank, the plumbing to your grow bed, the grow media itself, a pump, and water conditions (temperature and pH) matched to whatever fish species you plan to keep. Once that’s in place, you can introduce your fish. It’s smart to start with just a few — that way, if something goes wrong early on, you haven’t risked your whole stock. Goldfish are a popular starter choice because they tolerate rough conditions well. At this point you can optionally add a bottled bacteria starter to speed things along; skip it and the bacteria will still show up naturally, it just takes a few more days. Another shortcut is borrowing some used filter media from an already-established pond to seed your system with bacteria faster — just make sure that source pond is free of parasites first.

Once fish are swimming in your tank, test your water daily without fail. Ammonia needs to stay under 2.0 ppm, and nitrite under 1.0 ppm. Let either climb too high and your fish will show signs of stress or worse. If ammonia does spike past safe levels, hold off on feeding until the reading comes back down. You may also hear concerns about E. coli risk in an aquaponics setup — in practice, that risk is quite low.

Cycling With No Fish Involved

If you’d rather not put fish through the stress of a live cycle, fishless cycling is the alternative. You still need the full system built and ready to go, just as you would for cycling with fish. This time, add a bacterial starter product to kick off colony growth, then dose the water with ammonia until your test readings hit 4.0 ppm. Ammonia for this purpose comes in either liquid or powder form — either works. From there, test daily and top up ammonia as needed to hold that 4.0 ppm level, always testing right before adding more, with roughly 24 hours between doses. Once your readings show ammonia has fallen to about 0.5 ppm and nitrite is starting to show up in your tests, the bacterial cycle is underway and you can stop adding ammonia.

There are a few common sources of ammonia for a fishless cycle, described below.

Liquid Ammonia

Whatever liquid ammonia you use has to be pure — look for a concentration around 5-10% ammonia with nothing but water as the other ingredient. Anything else introduces extra chemicals that could harm your fish or plants down the line. This tends to be the least expensive route, though pure liquid ammonia can be surprisingly hard to track down.

Ammonium Chloride (Crystal Form)

This works essentially the same way as liquid ammonia but is much easier to source — most aquarium shops carry it, and you can even find it at some photography supply stores. It ships as a dry, highly concentrated powder, and it’s cheap to have shipped to you.

Urine

Human urine (or urine from any animal, really) is a strong natural ammonia source. People typically use their own simply because it’s the most convenient to collect. One important step: seal it in a bottle and let it sit for about three weeks so it fully converts to ammonia before you add it to your system. Skip that wait and you lose the ability to track how much ammonia you’re actually adding, which risks a sudden, dangerous spike. That sharp smell you notice when using the bathroom is the ammonia itself.

Using a Dead Fish

This isn’t a method worth recommending. A decaying fish doesn’t just raise your ammonia — it also introduces unwanted bacteria and other compounds into your water, and can attract flies. You’d also have a hard time controlling how much ammonia gets released, on top of needing to obtain a dead fish in the first place. If a fish dies in your tank and goes unnoticed, the same problem happens by accident: it decays, ammonia climbs, and bacteria you don’t want get introduced.

The Upside of Going Fishless

Fishless cycling tends to be quicker — typically 2-3 weeks compared to 4-6 weeks when fish are present from the start. That’s because you’re free to push ammonia levels higher to accelerate bacterial growth, without any risk of harming fish. It also means you can stock your tank with your full target number of fish right away, rather than building up gradually the way you have to with a fish-in cycle. Once your fishless cycle is complete, you’re ready to add fish — just hold off on feeding them for the first 24 hours. And remember, once fish go in, stop adding ammonia manually; the fish themselves now supply it.

Watch Out for the Nitrite Spike

A nitrite spike shows up in almost every cycling run. Once the ammonia in your system gets consumed, bacteria convert it into nitrite — and nitrite can actually be more harmful to fish than ammonia was. The bacteria responsible for turning nitrite into nitrate take longer to establish than the ammonia-converting bacteria did, so this stage can drag on. Don’t add fish until your nitrite reading hits zero — introducing fish while nitrite is still above 1 ppm puts them at real risk of dying.

Final Thoughts

Cycling your system properly sets up the right conditions for your fish, your plants, and the bacteria that connect them. Waiting four to six weeks before you can start planting can test your patience, but it’s a step you can’t skip. A properly cycled system means happier, healthier fish and plants that tend to grow faster, stronger, and with better flavor.

The good news: you only have to cycle a system once. After your bacteria colony is established, you can swap out plants or even fish over time without upsetting that balance. As your bacteria colony matures, it will naturally push your water’s pH down over time. So if you notice pH creeping upward instead, treat it as a warning sign that your bacterial colony may be shrinking. One of the most common causes of that decline is solid waste building up and clogging your grow beds — so if your pH starts climbing, check your grow beds for trapped solids first.