The Nitrogen Cycle

What Is the Nitrogen Cycle?

The nitrogen cycle is the essential biological process that makes an aquarium safe for fish. It is nature’s filtration system that quietly works inside our filters. That is why a filter is so vital for all living aquatic animals. Beneficial Bacteria colonies live in the porous areas in our filter media and break down toxic nitrogen waste produced from decaying fish waste and uneaten food.

Here’s the short version:

  1. Organic material decays and produces ammonia, which is toxic
  2. Beneficial Bacteria convert ammonia into nitrite, which is also toxic
  3. Different beneficial bacteria convert nitrite into nitrate, which is non-toxic in small amounts and can be food for some plants and coral.
  4. You remove nitrate through water changes or plants (in a freshwater planted aquarium).

Without the cycle, fish will die from ammonia poisoning within days.

This is why every aquarium must be fully cycled before adding fish.


The 3 Waste Nitrogen Compounds You Must Know

1. Ammonia (NH₃), Toxic

Produced by:

  • Fish waste
  • Decaying food
  • Decaying plants
  • Dead organisms

Ammonia burns the gills of fish and causes stress, disease, and death.

Safe level: 0.0 ppm


2. Nitrite (NO₂⁻), Toxic

Once ammonia appears, bacteria begin converting it into nitrite.

Nitrite prevents a fish’s blood from carrying oxygen.

Safe level: 0.0 ppm


3. Nitrate (NO₃⁻), Safe in low levels and food for plants and coral at the right level

Final stage of the cycle.

Fish tolerate it well, but it must be removed periodically because it can reduce dissolved oxygen levels at higher ppm.

Safe range:

  • 5–40 ppm is ideal, up to 40 ppm is acceptable for many fish
  • 5-20 ppm preferred for reefs, plants, and sensitive species
  • 60+ ppm can reduce dissolved oxygen in the water, making it hard for fish to breathe.

 

Meet the Bacteria:

1. Primary, ammonia-eating bacteria

Nitrosomonas
Converts Ammonia to Nitrite

2. Secondary, nitrite-eating bacteria

Nitrospira (or Nitrobacter in older literature)
Converts: Nitrite to Nitrate

 

These bacteria colonize:

  • Filter sponges
  • Bio media (ceramic rings, bio-balls, etc.)
  • Substrate
  • Rocks

 

How to Cycle an Aquarium:

Step 1: Set Up the Tank Completely

Install:

  • Substrate
  • Filter
  • Heater
  • Hardscape

Fill with dechlorinated water or properly salted RO/DI water if doing a saltwater tank.


Step 2: Add Your Ammonia Source

You need ammonia to “feed” the bacteria.

2 correct options:

  • Pure liquid or powdered ammonia
  • Fish food

Target starting ammonia: 2.0 ppm


Step 3: Add Beneficial Bacteria (Optional but Highly Recommended)

The best bacteria:

  • Fritz TurboStart 700 or 900

TIP: This product is the most expensive on the market, BUT it is delivered to order because it is a 100% live product that has a short refrigerated shelf life. This is the only product we’ve found that reliably works within a week or two. 


Step 4: Test Your Water Everyday

Use the API Freshwater or Saltwater Master Test Kit.

You will see a pattern:

Week 1-2:

  • Ammonia: rises
  • Nitrite: 0

Week 2-3:

  • Ammonia: starts dropping
  • Nitrite: rises

Week 3-6:

  • Ammonia: drops to 0
  • Nitrite: drops to 0
  • Nitrate: rises


TIP: If at any point ammonia rises above 4ppm, nitrite above 5ppm, or nitrate above 100ppm, the cycle will stall and not progress until a 50% water change is done to lower the amounts.


Step 5: When Both Ammonia & Nitrite Stay at 0

You are officially cycled.

This means your bacteria population is stable and can handle waste.

Perform an 80% water change to lower nitrate levels before adding fish.


How Long Does Cycling Take?

Depends on method:

With bottled bacteria: 7–21 days

Without any bacteria product: 4–8 weeks

With established media from another tank: Instant to a few days

 

How to Know for Sure Your Tank Is Cycled

A tank is cycled when: 1ppm of ammonia is processed in 24hours (ie, you add ammonia up to 1ppm, and 24hours later you test and it reads 0ppm)


How to Maintain the Cycle After It Starts

Do:

  • Perform weekly 25–40% water changes
  • Rinse filter media only in tank water
  • Keep the filter running 24/7
  • Avoid overfeeding and overstocking

DO NOT:

  • Replace filter media (this removes bacteria completely)
  • Rinse media under tap water (kills bacteria due to chlorine)
  • Turn off the filter for hours (drying media kills bacteria)
  • Overclean the tank (stripping bacteria from substrate)

 

Fishless Cycle vs. Fish-In Cycle

Fishless Cycle (Recommended)

  • Fast
  • Humane
  • Allows precision

IMPORTANT: Fish-in cycling is more complex, slower, and stressful for fish as ammonia BURNS them (just like smelling it burns OUR noses)


Saltwater vs Freshwater Nitrogen Cycle

Same chemistry, different surfaces.

Saltwater:

  • Live rock plays a huge role, just as the filter does
  • Corals consume some nitrate

Freshwater:

  • Filters and substrate handle most biological load
  • Live plants help significantly with nitrate removal

 

Common Mistakes That Kill or Stall the Cycle

❌ Using tap water (chlorinated water kills bacteria)

❌ Turning off the filter overnight (dries the bacteria to death)

❌ Replacing filter cartridges (throwing out bacteria)

❌ Not using enough ammonia to establish bacteria (a tank can produce up to 1-1.5ppm of ammonia per day)

❌ Adding fish too early (ammonia buildup will kill fish)

❌ Overloading new tanks with too many fish at once (a newly cycled tank is at high risk of crashing since the bacteria colonies are new)

 

How to Speed Up the Cycle (Safely)

  • Add established media from a healthy tank
  • Use bottled bacteria
  • Keep temperature at 80–82°F (bacteria love heat)
  • Aerate your tank (oxygen boosts bacteria reproduction)