Understanding the Biological Cycle of Your Koi Pond

The biological cycle is really better defined as the “nitrogen cycle” because primarily what pond keepers are concerned with is nitrogenous waste.  When it comes to elements, nitrogen is pretty common. In fact, it makes up almost 80% of our atmosphere so it’s not surprising that it should be found in many plants and animals, too. Nitrogen can be found in proteins and DNA as well as fish waste. The nitrogen cycle in your pond really has to do with what happens to the nitrogen in fish waste, decaying plant matter and uneaten food. The following is a step-by-step explanation of that process.

Koi Pond Waste Processing

1. In your pond fish excrete waste and maybe your koi munch the stalk off a submerged plant so it lies decaying on the bottom and there happens to be some uneaten food mixed in with everything else. These are not your only source of nitrogenous waste but they probably make up a large proportion of it. The first nitrogen-based chemical that will appear in your pond is ammonia.

This comes about because bacteria and some fungi will subsequently assimilate or break down the aforementioned “stuff” lying on the bottom of your pond -the by-product of which is ammonia. On the scale of harmful chemicals to your koi ammonia is number one.

2. In a koi pond with a good biological filtration system there will be nitrosomonas bacteria and these guys will take ammonia and oxygen and use it as fuel and turn it into a waste product called nitrite. On the scale of harmful chemicals to your koi nitrite comes in at number 2.

3. The next helpful bacteria in the cycle are called nitrobacter. These bacteria convert nitrites and oxygen into a waste product called nitrate.
4. The nitrates are then assimilated by another suite of bacteria that do not use oxygen, these are called “anaerobic bacteria”. They live in oxygen free parts of the pond and produce free nitrogen from nitrates.

Filter systems were discussed here but where do aquatic plants come into play? Plants, like submerged vegetation and surface vegetation (lilies), are critical parts of your pond’s ecosystem for their abilities to “suck up” nitrates, produce dissolved oxygen and block the sunlight that would otherwise help algae grow. So what is so bad about algae?

Algae is good on one hand because it produces dissolved oxygen which enters the water but algae also grow rapidly then die and once that happens you will end up with a lot of decaying algae in your pond. All the dead algae will drive up ammonia levels and lower oxygen levels.

Remember those nitrosomonas bacteria that use oxygen and ammonia to produce nitrites? The more decaying material, the more oxygen will be used up by bacteria leaving your pond with decreasing levels of dissolved oxygen.

If you would like to know more about water chemistry and how it affects your koi please see my article here.

5 thoughts on “Understanding the Biological Cycle of Your Koi Pond”

  1. My very very big fish that are around 15 to 25 inches are getting sores and dying. I have put in two huge filtration systems that filter upto 16000 gallons n my two ponds are only 1200 gallons and 2500 gallons respectively. Have put in dechlorinators, done salt water changes, put in meds, but to no avail. I am totally distraught, and don’t know what to do. Some of the fish are like 20 years old, cud it be old age, or stress. Can you help. Have checked water samples and they are perfect,

    • Having a similar problem. I understand Koi can live to be 200, in perfect conditions.
      Have a new 1600 gal pond built this spring with an under gravel filter ( I understand not the best). Figured I would give my (2) 18 year old koi and 7 goldfish a better home instead of moving them inside every winter.
      Starting having problems two weeks after I introduced the 2 koi and 7 goldfish. The white scaless koi (Doitsu) started flashing and developing sores and red streaking. At fist I suspected parasites, though the other fish were fine. I manage to remove him along with the other koi back to there original 155 gal concrete pond. I treated them with tetra pond fish treatment. Two days latter he was better. I returned them back to the larger pond after 2 weeks and in 3 days the sores reappeared. Water tested fine, Was doing water changes. Started to think he was hitting the stones. I then treated the pond with Melafix. The sores seem to be getting better. I am now thinking he is sensitive to the mulch and rocks used to build the pond. Who knows what was on them.
      Hope you were able to figure out what was causing your koi getting sick.
      Good luck!


    • Water change for starters and you have to get your water chemistry under control. What is your filtration like? One thing that helps is beneficial bacteria on filter media-it helps to assimilate nitrogenous waste like nitrates and nitrites.

  2. I would guess it might be aerimonus bacteria that is causing the sores (ulcers). They are naturally occurring bacteria in any pond but only appear as problematic if the fish have had their slime coats disturbed through injury, eg. like scale loss from your doitsu koi,or any parasite that has invaded the koi’s skin. This bacteria is opportunistic to such injuries. I have never been able to cure it once it is discovered and I euthenize affected fish so they don’t slough off more bacteria as they deteriorate. It’s too sad to watch and I have lost nine this spring.They were treated for “bugs” and also salt treated and given Melafix, to no avail. I use clove oil to put the fish peacefully to sleep.


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