Sanke koi with head poking out the water

Ammonia and nitrite may be the big killers in a koi pond, but almost as important as their removal is that of the other types of organic waste your koi produces. This is why proper and functioning mechanical filtration is critical.

We have often stressed the importance of water quality. Especially when it comes to the health of your koi. And in a bizarre twist, the koi themselves are the biggest contributors to the decline in water quality.

Your koi are poop machines. Without true stomachs, they excrete a lot of waste back into the system. This waste, along with undigested food, leaves (or other organic waste that makes its way into your pond) if not given the proper steps to remove the nitrogen- and carbon-derivatives, can overload your filtration system.

Organic matter, if not properly dealt with in your koi pond, can play havoc with water quality and your koi’s health.

Types of Mechanical Filtration

Settlement-style mechanical filtration

Generally this is a gravity-fed system where water is drawn into (or pushed down) into a chamber where the wastes then settle and can be flushed from there.

The better settlement system will have the water moving a little more slowly into its catchment area. The longer the water stays in the settlement area, the more efficient it is in siphoning off the particles or matter.

The size of the settlement chamber in relation to the amount of water that flows through it helps to control that settlement. But it has to be fine-tuned according to the size of the piping in your drain.  A solid rule of thumb is your settlement tank should be roughly 1/10th of your minimum water flow. 1,500gph – 150g tank, 2,500gph – 250g tank.

Diagram of a settlement chamber from a bottom drain
Diagram of a bottom drain and settlement chamber setup. Courtesy: Koi Answers


This requires the use of a particular type of media that is closely pressed together to catch the solid waste as water is forced or runs through it. Once the media gets dirty, it can be cleaned, rinsed and backwashed (depending on the type of filter being used) to make sure that the organic matter doesn’t begin to decompose in the filter itself.

There is no such thing as “too much filtration” but there is definitely too little of it. Always err on the side of more is better. Setting up filtration in series with solids being removed and then nitrogenous wastes (ammonia, nitrite and nitrate) next is a good system. Some people even set up bogs, in conjunction! Some filters can do it all in one. But it is not a function of the size of your pond, but rather what your bioload is.

Here are some of the different types of mechanical filtration systems available to koi enthusiasts.

  • Bottom drains and settling chambers.
  • Rotary drum
  • Skimmer
  • Vortex
  • Bead
  • Brush
  • Foam
  • Sand
  • Sieve

Some of these types of mechanical filters used in koi ponds can even be run in a primary and secondary setup. For example a vortex style filter (which will remove up to as much of 80% or so of waste) can be used to syphon off most of the solid waste and then brushes can be used in a secondary capacity to filter off the remaining 20%)

Dead Spots

Perhaps not the most encouraging name for a portion of your pond or filtration efforts, nevertheless it is an area on your pond where wastes can coalesce and decompose without making it into your filter, thereby directly affecting your water quality.

What to do? There are options. Forced air from the bottom drain can help to create a current that pushes the solid waste down and towards the drain. Once you have identified this area, you can lightly brush the waste with a soft brush (potentially resuspending the particulates), use a net or get the pond vacuum out. It can depend on the shape and type of pond you have.

High quality food is a blessing and a curse. As your koi doesn’t have a real stomach it essentially only filters out the nutrients that it needs in the moment. The rest of it is just pushed back out into the water. So as it gets the quality nutrition it needs, it also releases the concentration it doesn’t need into the surrounding environment.

One thing is for sure though, you need to maintain your filtration system. It is not a setup-and-sit-back scenario either. Regular cleaning of your mechanical filter is of massive importance. The exception is the rotary drum, which requires almost no maintenance.

It is possible to inadvertently affect your water quality, too. If you don’t clean your filters properly or often enough (the beads, mats, brushes, sand or other type of scrubbing media), the nitrifying bacteria that remove waste products can build up to dangerous levels on the decomposing solids trapped in the media and then be reintroduced in larger numbers into your pond water.

Issues from Incorrect/Improper Mechanical Filter Cleaning

We also stipulated that Aeromonas is in EVERY pond. Period. They are a necessary and useful bacteria in maintaining healthy water parameters by helping to break up the chemical waste products, most specifically Ammonia.

When kept in check, they provide a vital service. But if they grow to large numbers, these opportunistic pathogens then become a danger to your koi, causing Ulcer disease in those fish with weakened immune systems.

Guess who else loves high concentrations of organic material? Parasites. Especially the ectoparasites (flukes and protozoa) that thrive in a high bacteria environment. Not having a well-filtered pond can encourage and enable a parasitic infection, too.

And then there is algae. Not the good stuff that helps with waste, the blooming kind. The string kind. A lot of waste will result in increased levels of non-organic byproducts, like phosphate and nitrate. Algae thrives on these left overs. Algae also plays havoc with your dissolved oxygen

There are hundreds of different filters and styles of filtration. Enthusiasts will swear by one style of mechanical filtration versus another. It is a hotly contested topic. But the bottom line is getting your water clean with good parameters. How you get there can be trial and error. A clean filter is a happy filter. And more importantly, a healthy filter. One that gives back to the water and the koi in it.

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