Understanding the Nitrogen Cycle (Ammonia, Nitrite & Nitrate Explained)

Understanding the Nitrogen Cycle (Ammonia, Nitrite & Nitrate Explained)

If youve kept fish for any length of time, youve probably heard people say a tank needs to be "cycled." This is what they mean: your aquarium needs a working colony of beneficial bacteria that turns toxic fish waste (ammonia) into something less toxic (nitrate). The nitrogen cycle is basically your tanks built-in waste processing system.

Once you get the cycle, a bunch of aquarium mysteries stop being mysteries. Fish gasping even though the filter is running? A sudden spike after you cleaned the filter too hard? A tank that was "fine" for a week and then crashes? Thats usually the cycle (or a broken cycle) showing itself.

The three main players: ammonia, nitrite, nitrate

Think of these as stages of the same waste moving through your tank. Youll see them in a specific order during cycling, and youll test for them when youre troubleshooting.

Ammonia (NH3/NH4+)

Ammonia comes from fish poop, uneaten food, decaying plants, and even just fish breathing. It can burn gills fast, and it can hit you out of nowhere in new tanks. The tricky part is ammonia is more dangerous at higher pH and higher temperature.

Nitrite (NO2-)

Nitrite shows up after ammonia bacteria get established. Nitrite messes with oxygen transport in fish blood (people call it "brown blood disease"). Fish can look like theyre suffocating even when theres plenty of oxygen in the water.

Nitrate (NO3-)

Nitrate is the end product in most aquariums. Its much less toxic than ammonia or nitrite, but it can stress fish long-term at high levels and it tends to fuel algae. Nitrate is also your clue that the cycle is working: if you consistently get nitrate readings, your bacteria are doing their job.

Where the beneficial bacteria actually live

People say the bacteria live "in the water," but most of them live on surfaces. Your filter media is the big one because water constantly flows through it. They also live on gravel, rocks, driftwood, plant surfaces, and even the glass.

• Filter media (sponges, bio rings, ceramic media) is prime real estate
• Substrate and hardscape hold a lot of bacteria too
• The water column holds some, but its not your main biofilter
• Replacing all filter media at once can crash or weaken your cycle

What cycling really means

Cycling is just growing two main groups of bacteria (and other microbes) that do two conversions: ammonia to nitrite, then nitrite to nitrate. In a brand new tank, those colonies are tiny. Your job is to feed them and give them time.

A tank is "cycled" when it can process a steady waste load without measurable ammonia or nitrite showing up between water changes. Youll still get nitrate, because thats where the chain usually ends.

Fishless cycling (my preferred method)

If you can do fishless cycling, do it. Its calmer, cleaner, and you dont have to babysit fish through toxic spikes. You add an ammonia source to feed the bacteria, test regularly, and wait for the bacteria to catch up.

What you need

• A liquid test kit for ammonia, nitrite, nitrate (strips can work in a pinch, but liquid is easier to trust)
• A steady ammonia source (pure household ammonia with no scents/surfactants, or fish food as a slower method)
• A running filter and heater (bacteria grow faster in warm, stable water)
• Patience and a notebook or phone notes for test results

Step-by-step fishless cycle

1. Set up the tank fully: filter running, heater on, dechlorinator used. Get temperature stable.
2. Add ammonia (or a small pinch of food if youre doing the slower food method). Your goal is to create measurable ammonia for the bacteria to eat.
3. Test ammonia and nitrite every day or two. At first youll see ammonia and no nitrite.
4. After a while, nitrite appears. Thats progress. Keep feeding ammonia lightly so the first bacteria dont starve.
5. Eventually youll see nitrite start dropping and nitrate rising. Thats the second group showing up.
6. Youre close when ammonia goes to zero quickly and nitrite also goes to zero quickly after dosing ammonia. Nitrate will climb.
7. Do a big water change to bring nitrate down before adding fish, then stock gradually.

Fish-in cycling (if you already have fish)

Sometimes you inherit a tank, or a store sells you fish before you knew better. Fish-in cycling is doable, but you have to stay on top of testing and water changes. The goal is simple: keep ammonia and nitrite as close to zero as you can while the bacteria catch up.

1. Test ammonia and nitrite daily at the start.
2. Feed lightly. Most cycling problems get worse because of extra food rotting in the tank.
3. Do water changes whenever ammonia or nitrite show up. Big enough to bring the numbers down noticeably.
4. Use dechlorinator every time. Chlorine/chloramine can hurt fish and your growing bacteria colony.
5. Add extra aeration (an airstone or higher filter agitation). Toxic spikes and warm water both make oxygen more valuable.

How long cycling usually takes

Most tanks cycle in a few weeks to a couple months. Ive seen it move quickly with seeded media and warm water, and Ive seen it crawl when the tank is cold, the filter is weak, or ammonia is swinging all over the place.

• Warm, stable temps (mid 70s to low 80s F) generally speed bacteria growth
• Seeded filter media from an established tank can cut the wait dramatically
• Constantly changing or overcleaning filter media slows everything down
• A brand new tank with no seed material often takes the longest

Seeding a tank to speed things up

If you have a friend with a healthy aquarium, a piece of their dirty sponge or some established bio media is gold. Youre basically borrowing a ready-made bacteria colony. Just make sure the source tank is healthy and not dealing with disease.

• Best: a chunk of established sponge filter or a bag of mature ceramic media placed in your filter
• Good: squeezing gunk from an old sponge into your filter area (messy, but it works)
• Less useful: a cup of gravel moved over (still helps, just not as strong as filter media)

Testing: what to look for and how to read the story

Your test kit is basically your window into the cycle. During a normal cycle you usually see: ammonia rises, then nitrite rises, then nitrate rises, then ammonia and nitrite drop to zero while nitrate keeps accumulating.

Typical cycling pattern

• Phase 1: Ammonia present, nitrite at zero, nitrate low
• Phase 2: Ammonia starts to drop, nitrite rises, nitrate starts to appear
• Phase 3: Nitrite drops, nitrate rises steadily
• Established: Ammonia = 0, nitrite = 0, nitrate rises between water changes

Common test kit gotchas

• Nitrate tests often need aggressive shaking (follow the bottle directions exactly)
• Rinse tubes with tank water after testing to avoid contamination
• Check expiration dates and store reagents out of heat and sun
• Test tap water too, especially if your tap already contains nitrate

What messes up the cycle

A cycled tank is pretty stable, but you can still knock it back. Most cycle problems I see come from good intentions: deep cleaning everything at once, replacing all media, or making big stocking changes quickly.

• Replacing all filter media at once (you just threw away your bacteria)
• Rinsing filter media under tap water (chlorine/chloramine can kill bacteria)
• Overcleaning the substrate and filter in the same day
• Adding too many fish too quickly
• A long power outage where the filter sits stagnant (bacteria can die back)
• Medications that affect bacteria (some can reduce your biofilter)

Ammonia spikes in an established tank

If your tank has been running for months and suddenly you detect ammonia, something changed. The bacteria either got reduced, or the waste load jumped.

• Dead fish or hidden decay (check behind hardscape and inside decor)
• Overfeeding or a food block melting into mush
• Filter clogged and flow slowed way down
• Filter media replaced or cleaned too aggressively
• Sudden stock increase or a big messy fish added
• Substrate stirred heavily, releasing trapped waste

The role of plants

Live plants can make nitrogen feel boring, in a good way. Fast growers and floaters especially pull ammonia and nitrate out of the water as fertilizer. They dont replace your biofilter, but they smooth out the bumps.

• Floaters often suck up nutrients fastest because they have unlimited CO2 at the surface
• Stem plants help a lot once theyre growing steadily
• Dying leaves still add waste, so trim melt and rot promptly
• Heavily planted tanks can show low nitrate even when cycled - thats normal

Water changes and nitrate control

Nitrate is the one you manage long-term. My approach is simple: test periodically, watch your tanks trend over time, and use water changes to keep nitrates reasonable for the fish youre keeping.

• If nitrate creeps up week after week, increase water change volume or frequency
• If nitrate is already high in your tap water, you may need plants, lighter feeding, or alternative water sources
• Dont chase a magic number - watch fish behavior, algae, and consistency

pH, temperature, and why ammonia toxicity changes

Ammonia comes in two forms in water: NH3 (more toxic) and NH4+ (less toxic). Higher pH and higher temperature shift more of it into the toxic NH3 form. Thats why the same ammonia test reading can be a bigger emergency in a warm, high-pH tank than in a cooler, lower-pH tank.

Chlorine, chloramine, and dechlorinator

Tap water treatment matters because it can wipe out bacteria and irritate fish. Chlorine gasses off, but chloramine (used by many cities) sticks around and needs a conditioner. Always treat new water before it hits the tank, especially during cycling.

• Use a dechlorinator that handles both chlorine and chloramine
• If you do big water changes, dose for the full tank volume if the product directions call for that
• If you suspect a change in your water supply, test and adjust rather than guessing

Cycling with different filter types

Most filters can run a cycle just fine. The difference is how much bio media they hold and how stable they are when you clean them.

• Sponge filters: simple, hard to mess up, great bio filtration for the size
• Hang-on-back: good, but avoid tossing cartridges; keep a sponge or media you can rinse and reuse
• Canister filters: lots of media and very stable, but dont deep clean everything at once
• Internal filters: can work well in smaller tanks; keep an eye on flow and clogging

How to know your tank is cycled

Youll know its real when the tank behaves the same way for a while, not just on one lucky day. In a cycled tank, ammonia and nitrite stay at zero, and nitrate rises gradually until you dilute it with water changes or plants use it up.

• Ammonia reads 0 consistently
• Nitrite reads 0 consistently
• Nitrate is present and increases over time (unless plants are consuming it fast)
• Fish act normal and you dont get mystery stress after feeding
• Filter flow is steady and maintenance does not cause mini-spikes

Stocking after cycling

Even after a fishless cycle, I still add fish in stages. The bacteria colony adjusts to how much waste is available. Dumping a full stock list in at once can outpace the biofilter you just built.

1. Add the first group of fish.
2. Feed lightly for the first week and test ammonia and nitrite every day or two.
3. If readings stay at zero, add the next group.
4. Repeat until youre stocked where you want to be.

Quick troubleshooting guide

Ammonia wont go down during fishless cycling

• Check dechlorination (chlorine/chloramine can stall bacteria growth)
• Make sure the filter is running 24/7 with decent flow
• Raise temperature a bit (within safe range for your setup) to speed bacterial growth
• Dont overdose ammonia - keep it moderate and steady
• Consider seeding with established media

Nitrite is stuck high for weeks

• This is common - the second stage often takes longer
• Keep feeding ammonia lightly so the first stage bacteria dont starve
• Do partial water changes if nitrite is extremely high (yes, even in fishless cycling) to keep things from stalling
• Double-check your nitrite test accuracy and expiration

Nitrate is sky-high

• Do a large water change (or several over a few days if you need to be gentle with sensitive fish)
• Reduce feeding and remove decaying plant matter
• Add fast-growing plants or floaters if you like planted tanks
• Test your tap water for nitrate so you know what youre starting with

A simple mental model that helps

I picture the nitrogen cycle like a conveyor belt. Waste goes on as ammonia. The first bacteria station turns it into nitrite. The second station turns nitrite into nitrate. Your job is to keep both stations staffed (dont throw away media), feed the belt at a reasonable rate (dont overstock/overfeed), and remove the finished product (water changes and plants).

Key takeaways

• Ammonia and nitrite are the immediate dangers. Nitrate is the long-game number.
• Most beneficial bacteria live on filter media and surfaces, not floating in the water.
• Cycling has two steps: ammonia to nitrite, then nitrite to nitrate.
• Test kits save fish. Guessing causes problems.
• Avoid replacing all filter media at once or rinsing it under tap water.
• After cycling, add fish gradually and keep an eye on your numbers for a couple weeks.