Understanding Koi Pond Filtration

Koi Pond Filtration: The Basics

Koi ponds and koi keeping are gaining popularity in the U.S. and in many parts of the world. Koi ponds are as varied as the places they are found. Ponds can be deep or shallow, be natural or constructed with liners or concrete but no matter what form they take the filtration system of the pond will always be universally vital to the health of the resident fish. If you are unsure where to start when it comes to understanding a koi pond filtration system, this article is meant to give you an overview and a place to start.

pets by popularity
Ranking Pets by Popularity

Koi produce waste that could be classified as both chemical and physical so as you can imagine it only makes sense that your pond will need to have the ability to handle both. The two main types of filtration are biological and mechanical. Biological filtration cultures aerobic (nitrifying) bacteria that will help break down the chemical components of fish waste. Mechanical filtration is employed to handle the physical waste like fecal matter, dead leaves, dead insects etc.

Setting up your Pond

There are specific elements you need to have present in your pond to ensure the health your Koi. Before delving into filtration, you should have an understanding of the basic components of the pond and their purpose.

Bottom Drain

Most ponds will have a bottom drain. For the sake of the natural path of debris and waste that falls to the bottom with gravity, the bottom drain is often positioned at the deepest point of the pond.   Ponds without a bottom drain will have to deal with wastes building up and causing muck that will have to be removed at a later date (like every Spring) or regularly vacuumed out. The bottom drain will lead to a settlement tank.

The water flowing into the bottom drain will move into a settlement tank, which is then allowed to settle to the bottom of the tank while the surface water is sent towards the pump. In between the tank and the pump will be a filter, such as a bio filter. This filter helps remove more waste from the old water, ensuring cleaner water is then pumped back into the pond.

You will need to ensure the flow rate of the water matches up the bottom drain pipe size. A slow flow rate will cause the heavier particles to settle in the bottom drain piping instead of moving into the settlement tank. However, you need a flow slow enough that it allows heavier waste to sink while in settlement tank.

To help you figure out the proper bottom drain configuration, consider a three inch bottom drain, which is able to sweep a 4 foot radius. In order to work, this drain needs a minimum water flow of 1500 gallons per hour, so the sediment will not settle in the piping. It is better to have 2,500 gallons per hour with a 150 gallon settlement tank when using a three inch bottom drain.

A four inch bottom drain is ideal and can sweep a six foot radius and requires at least 2,500 gallons per hour for a 250 gallon settlement tank. In order to ensure that your settlement tank will do its job properly, a good rule of thumb is to match your settlement tank volume to your minimum water flow at a value of 10% -in other words, your settlement tank volume should be about 10% of your gallons-per-hour water movement.

bottom-drain for koi pond
Typical bottom drain

Gravity obviously does a lot to get the sediment and waste into the settlement tank. Once the water is in the tank, the solid waste will remain unable to move beyond the tank until the pump suctions off the settlement tank.

The settlement tank will require a little help from you. While most of your pond can be kept clean with the bottom drain and skimmer, there is also a need for some maintenance. You should get into the habit of checking the settlement tank filter every other day or so. The waste container will fill up and needs to be dumped. It is your job to make certain this happens on a regular basis.


The bottom drain, as the name implies, is at the bottom of the pond however another form of filtration often seen in ponds is the skimmer. Skimmers are your other mechanical filtration system. The skimmer works on the top of the pond collecting floating debris such as leaves, grass, pollen and the like. The skimmer will pull from across the top of the pond collecting waste, filtering the water back to the pump.

Ranking those two systems in order of importance, the bottom drain would certainly be first. Floating debris will effectively be removed via the skimmer, but without it all things would ultimately make it to the bottom drain.

The skimmer also removes dissolved organic compounds. If you do not have a skimmer, the surface of your pond may end up with an oily film, which will reduce the ability of atmospheric oxygen to diffuse into the pond via the water’s surface.

typical pond skimmer
Typical Pond Skimmer

The skimmer has a weir or a floating device that floats up and down with the water level. It skims only the surface of the water. If building a new pond you want to get the widest weir available, at 16 inches, to help clean the pond surface area quicker. The skimmer also has a “leaf basket,” which collects the large debris. Some skimmers may have netting or mats, but it works the same way. It ensures the debris cannot cloud the surface of your pond or get into the pump.

Mechanical Filtration

This type of filtration is one of two main kinds of filtration going on in your pond. At its simplest, fish produce both liquid and solid waste which represents both a physical addition and chemical addition to the pond. As a result, a pond owner needs both physical and chemical means of removing these wastes from the pond.

Of course, there are other sources of nutrients like rainwater runoff, decaying plant matter, dead insects etc. as well as other sources of solid wastes like dead leaves, branches, pollen etc. Additionally, those solid wastes come in different sizes and need to be filtered out accordingly therefore a good mechanical filter will have multiple stages.

Typically these stages are set up such that water carrying particulates pass through the largest pored filter material first then gradually each stage’s pore size gets smaller to trap smaller particulates. Let’s look at a typical multi-stage mechanical filter.  As you can see from the image, as the water enters it is met by coarse filtration, then finer filtration, and then even finer filtration etc. until making its way to biological filtration.

example of mechanical filtration

Biological Filtration

The biological process of beneficial (nitrifying) bacteria assimilating nitrogenous waste is natural and occurs in the wild, as well as in your own pond. When your fish produces waste it eventually turns into ammonia, nitrites and nitrates.

If there is an improper biological filtration in your pond, it can leave your pond with an excess of these waste products which ultimately reaches a point of toxicity—killing your fish. Biological filtration is an aerobic process, meaning oxygen is involved.

Ammonia is broken down into nitrites. A second type aerobic bacteria will take the nitrites and break it down into nitrates. At low levels, nitrates are harmless to your fish but regular water changes are also a good idea (assuming the volume of water changed out is small enough that is doesn’t cause signigicant pH swings).

The name of the game when it comes to setting up your biological filtration is surface area.   There are varying approaches to achieve high surface area filter media and these include porous rocks, ceramic rings, bio-balls and other plastic shapes that yield a high surface area.   So why all the need for surface area?  

A few beneficial bacteria assimilating your pond’s nitrogenous waste is good but a lot of bacteria is great so having a lot of surface area for these bacteria to live and thrive means that your biological filtration is that much more powerful.

For biological filtration, you want an oxygen rich environment so that the aerobic bacteria are able to assimilate the nitrogenous waste as efficiently as possible. To ensure this happens you need a pond with a large surface area and plenty of supplemental oxygenation via waterfalls, fountains, aquatic plants or diffusers.

When considering the right filtration system for your pond you will want to keep in mind that the entirety of your pond’s volume should be filtered every hour so choose a pump capacity/speed and filtration that will meet that goal. Let’s now take a look at some of the popular filtration systems to give you an idea of what’s out there and how they look when set up.

External Pressure Filters

The external pressure filter system is a common one and typically consists of an intake in your pond (usually sits on the bottom) that draws water in then up through a line, out of the pond and into the pressure filter itself.

There are many different designs in the world of pressure filters but essentially you will find some manner of mechanical filtration (usually in the form of a sponge-like material) which then leads to biological filtration (usually in the form of bio-balls) then out of the filter. Some manufacturers will also have a UV light installed such that the water exiting the pressure filter passes by the UV prior to leaving the filter.

From the filter it will often enter back into the pond via a water fall. They are nice systems that can be hidden out of sight either in a false rock or in an accessible, sub-terranian compartment. As with any filtration system outfitted with mechanical filtration you will have to periodically rinse off the sponge material catching the particulates. See the diagram below for the typical set up on these style systems.

submersible pump plus external pressure filter


The all-in-one systems like the Lifgard Aquatics example shown are often submersible units that have the mechanical filtration, biological filtration, UV clarifier and pump all in one compartment. So in the given example, this unit has an extended neck that then directs the filtered and clarified water into the fountain feature thus aerating the water.

lifegard all-in-one filter (triple)

Multi-Stage Compartment Filters

These filtration systems are external and designed quite simply. Its essentially a plastic box with mulitple sheets of filter media arranged in a pattern of coarse to fine. Some units, like the Matala Biosteps series, will have a UV clarifier in the first compartment before going through the stages of filtration.  

Other manufacturers will put bioballs as the last stage however the 4 staged filter material in the Matala are also meant to act as substrate for the beneficial bacteria to colonize. Cleaning units like this is a simple matter of shaking off any debris clogging the filters, allowing it to settle to the bottom then purging the waste out through the bottom drain. In the case of these progressive, multi-stage filters the water drawn through the system is either pumped from a submersible at the bottom of the pond or an external pump draws it up from the pond.

matala biosteps 10 filter

Ultraviolet (UV) Filtration

A somewhat newer addition to the koi pond filtration arsenal is the UV sterilizer/clarifier. The UV filter has been mentioned on multiple occasions in this article as it has gained increased popularity over the years. You’ll see a lot of different filtration systems with UV as part of the package as well as in-line UV sterilizers and clarifiers too.

In essence, what happens is that pond water is passed over/near a UV light source and the ultraviolet light energy effectively disrupts the chemical bonds that bind the microorganism’s DNA together. As as result, the bacteria, virus, protozoans, algae, or mold effectively die.

whats in a drop of pond water

The cool thing about UV is that is leaves no chemical residue or impurities in the water.   Its just light energy that is strong enough, and at the right spectrum, to kill microorganisms and requires only a bulb change when it becomes too weak to kill. The UV sterilizer/clarifier is typically placed before the mechanical filtration as it tends to cause free floating algae to clump together.

UV sterilizer vs. UV Clarifiers

The difference? Well, not much. Clarifiers go as far as killing free floating algae that causes green water whereas a sterilizer gets at the other nasties in the pond such as viruses, bacteria, protozoans etc. A single in-line UV light for a small pond might be a sterilizer whereas that same light at a pond 3 times bigger might be considered a clarifier.

It really comes down to wattage (strength) and flow rate (which will dictate how long the water gets exposed to the UV light). Other important factors are your biological load already present in the pond. Do you have lots of fish or an appropriate amount?  

Do you already have natural filtration going on in the form of aquatic plants? What is the volume of water in your pond? Big ponds need stronger UV exposure. To determine what your pond’s needs are its simply a matter of taking into account several key factors and using the chart below as a general guide.  

UV bulb sizing chart

UV balasts and bulbs are not necessarily cheap so is it worth it?   Viruses and bacteria make up a large proportion of health problems in any given koi pond. Many koi pond problems stem from water quality issues which then translate into koi health problems as well as algae blooms. Fortunately, UV kills green water (free floating) algae which can infest your pond, die then cause a spike in nutrients and a drop in dissolved oxygen.

One-bacteria-under-ideal conditions

There is even a “major trend in swimming pool technology” being seen across the U.S where UV is being used in more and more pools which underscores the effectiveness of UV to kill unwanted, water-borne microorganisms. So the cost up front may very well save you plenty of money and headaches down the road.

Ion Filtration

Even newer than UV is the use of Ion Filtration. Its a compact, easy to set up system that effectively kills free floating algae, viruses and bacteria. The way it works is this: a flow chamber containing two anodes (elongated, rectangular metal blocks) have a low voltage current going to them.   The anodes are made of copper, silver and zinc (though some are just copper and silver).

When there is an electric charge applied to the anodes they give off billions of positively charged ions of silver and copper.   Because unwanted things like algae, fungus spores, viruses and bacteria are negatively charged they are attracted to the positive ions. The copper ions are able to damage the cell walls enough that the silver ions get in there and destroy the cell.

Because the electric charge is so minimal and localized to the in-line ionizer in your pipes there is no adverse affect to your fish nor is there residual copper or zinc in tests of the water. Also because it draws such little power its very inexpensive to operate. The anodes will eventually become worn out and require replacement every year or so.

Aquascape IonGen ionizer plus diagram

Ozone Filtration

Disinfection of water via ozone has actually been around since the late 1800’s so its not surprising to see it in use in koi ponds (or where ever water needs to be sanitized). Ozone is arguably the most powerful destroyer of bacteria and viruses in the world of aquatic disinfection. In fact, its 50% more powerful than chlorine and yes, it kills algae cells too.

As with many forms of filtration mentioned above, there is no residue left over. In fact, the water is left super clean and more oxygenated because ozone breaks down into oxygen. Furthermore, only ozone can break down hydrocarbons like derivatives of oil and gas.   So how does this all work?

Air is passed through the Ozone generation mechanism where electric current is applied resulting in the creation of ozone gas. This gas is them pumped into a special chamber where it is allowed to diffuse into the water. Immediately hydrocarbons, viruses, bacteria, and other pathogens are destroyed and the action of ozone destroying these unwanted nasties converts it (ozone) back into oxygen thereby further oxygenating the water. Your fish never come in contact with ozonated water as it all takes places in a sectioned off area or a special chamber.

Natural Plant Filtration

Possibly the easiest filtration to implement in your pond is the oldest kind…aquatic plants. They are the gift that keeps on giving…and they grow and multiply. Besides the important filtration work they do naturally they also provide shade for your koi as well as substrate for female koi to attach eggs to.

They also add dissolved oxygen to the pond as well. Depending on your pond’s design you can install submerged plants, floating plants or plants partially submerged that sit on a shelf or shallow area.   Some favorites among pond owners are water purslane, fanwort, American Waterweed, iris, lotus and lilies. You will have to match the plants you get to your climate zone and pond design but aquatic plants add a great deal of functional value as well as aesthetic value to your pond.

koi pond cut away how pond plants benefit your pond final 3
Besides the aesthetic beauty of pond plants there are many other benefits to your koi pond


The aim of this article was to give you a good place to start in understanding koi pond filtration and all the different ways your water can be filtered to give your koi the best environment possible.  No one pond will have all these types of filtration but it will be up to your situation, space and finances to determine what filtration system(s) is going to be the best fit for your pond.  No matter how you slice it though, filtration is important so make sure you put the kind of time and effort into it that it deserves -your fish will thank you!

13 thoughts on “Understanding Koi Pond Filtration”

  1. i just found out the home i mght be purchasing has a koi pond in the back yard it about 10 feet long depth I DK? the water is mirky though there are koi fish in it that the current owners will take there’s alittle water spout in the middle of it and a water fall thats barely working? how do you clean it up and make the water clear again??? change the filters and clean up the soot??? where do you start?? thank you

    • Sorry for the late reply
      1) check the water chemistry (ammonia, nitrites, nitrates, pH, etc.
      2) clean filter and add something to boost your beneficial bacteria load (Microbe-Lift PL
      3) do several water changes
      4) lots of algae? try Green Clean. its great and works fast.
      5) still cloudy? try koi clay- its natural and effectively clumps particulates so you can vacuum them off the bottom.
      6) got a bottom drain? you need to find that out because it makes like easier it you have one.

  2. I have a bottom drain filter and it keeps getting clogged. Is there a way to keep it clear? I think the installers just have an open hole at the bottom. Is there a screen or cap that should have been put there?

    • Right so there should be a cap that rises above the intake that creates a finite space between the bottom and the underside of the cap and that restriction will block a lot of larger objects that can cause clogs. A quick fix type solution is a milk crate over the bottom drain.

  3. Thank you for the far reaching practical advice. I have been at it, koi keeping, for several years and still have murky/green algae water in my 4,000 gallon pond. I know it isn’t detrimental to my koi but I am determined to have clearer water. Have recently reduced my koi amount to about 25 feet/ 300 inches, added more mechanical filtration to my tanks and added irises to my stream. After mechanical filtration the water is partially diverted to about six cubic feet of Spirex trickle filtration before entering the 60% shaded pond.
    Once again, thank you.
    Tony Fellela

    • How is your water quality? If the fish is gasping that could mean high ammonia. It could also mean insufficient aeration.

  4. I plan a water plant pond (water lilies, some marsh orchids, other botanical-interest plants) with a few fish (as opposed to a fish pond with a few plants). Can I ignore the filtration aspect then? I suspect a skimmer will be advantageous, some sort of slow circulation pump, and an air pump. How about the rest?

    • Yes, you could probably get away without artificial filtration. It would help if you added some beneficial bacteria like Microbe-lift PL. They colonize all the little cracks and crevices on your pond’s substrate and help to further assimilate fish waste products.

  5. The filter isolated and removes the wastes. It’s working like a vacuum cleaner. It cleans the wastes things from the pond and makes the pond more clear. There are many types of filtration. Nowadays, the sieve and RDF are most popular. These tow filter use 200-300 micron sized screen to filter water. Any small particles can be removed by this system.

    Great explanation. Keep it up. Thanks!

  6. Pond filtration is one of the most important matter for a pond. For keeping clean a pond it will need a good filtration system. We all have to know that how to adjust a pond filter. I have got a lot of information in this article. Nice explanation.

  7. I have a small plastic pond in ground. My filter is outside the pond and a pump pulls the water up and another hose from filter goes back into pond. My waterfall is gone now and my husband put return hose back into water. Will fish get enough oxygen this way or should I have the return hose out of pond for water to hit air before going back into pond. I don’t have any plants now and I have a cover over pond to keep racoons out. It’s a frame with chicken wire. So I can’t have plants growing up . Thank you
    Sandi LaRue

    • Sandi, great question. When water flow breaks the surface of the pond, it creates agitation, which adds oxygen. More oxygen is always better than less oxygen, for Koi. I would rather error on the side of caution, and have the return line break the surface of the pond. Hope that helps!


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