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 For Beginners

  Filtration Systems
For Water Gardens and
Koi Ponds
Natural, Biological, Mechanical

by Joel Police
New Haven, Indiana USA

 Author’s Note: These articles are intended as general reference only. The information presented represents my perspective gained from experience as a water gardener and as a business owner. The views expressed here are also influenced by the conditions found in the Midwest and may not be as applicable in other geographic regions.

Materials and Components for Your Pond examined various building blocks that constitute water features, water gardens and koi ponds. There I omitted two topics, filtration and pumps, so that I could give an in-depth analysis for each subject. This article focuses on filtration systems for water gardens and koi ponds. The principles applicable to water gardens and koi ponds easily adapt to water features, but on a smaller scale.

The concept of filtration is very straightforward. A good filtration system keeps an aquatic ecosystem clean and free of harmful pollutants while reducing maintenance. Nonetheless, filtration systems require a significant investment of time and effort to keep a pond in balance. This means more than just turning on a garden hose and topping off the pond occasionally.

Even with massive daily water changes, filtration (natural and/or constructed) still would be necessary. A good filtration system protects the pond inhabitants against harmful pH swings, toxic ammonia levels and diseases besides keeping the water crystal clear. To understand the value of such a system, you need to understand the intricate processes working in a pond ecosystem.

The Nitrogen Cycle

The nitrogen cycle is the biogeochemical series of changes in nitrogen and nitrogen-containing compounds taking place in ecosystems. Fish consume and digest food, then excrete waste in the form of ammonia. Their respiration absorbs oxygen and releases carbon dioxide. Specialized species of aerobic bacteria (Nitrosomonas) break down ammonia into nitrites (NO2-). Other varieties of aerobic bacteria (Nitrobacter) process nitrites into nitrates (NO3-). Aquatic plants (including some algae) photosynthesize nitrates and carbon dioxide into food, releasing oxygen as a byproduct.

The process persists as long as a proper balance exists between fish load, oxygen content and filtration capabilities. If one factor goes out of balance, such as too many fish, the cycle crashes. Pond design, stocking levels, water volume, turnover rate and other factors put specific demands on a filtration system. You should understand nitrogen cycle basics before designing or installing your filtration system.

A good filtration system optimizes beneficial bacteria growth to eliminate as much ammonia as possible. What filtration choices do you have?

Mechanical Filtration*

Filtration breaks down into two distinct categories. Mechanical filtration removes physical debris; biological filtration eliminates chemical impurities.

Mechanical filtration catches large particulates like leaves down to fine debris suspended in the water. It does not change the debris; it simply traps solid material. A good mechanical filter clarifies water, prevents debris buildup and facilitates proper conditions for biological filtration.

Biological without mechanical filtering is a recipe for disaster and vice versa. Mechanical filtration alone cannot prevent toxic ammonia and nitrites from reaching lethal levels. Conversely, debris can soon clog a biological filter causing death to beneficial bacteria colonies. Comprehensive filtration fulfills both functions.

Just as a pond consists of various components, the same applies to filtration. A simple system includes a pump to move water, a mechanical filter, a biological filter and a means of aerating water via a fountain, waterfall or air pump. As the need arises, add more components to create a filtration system suited to your specific ecosystem and its needs.


The first line of defense in combating pond debris is a pre-filter. Often found on small submersible pumps (addressed in my next article), they consist of foam or other coarse sponge-like material. Pre-filters keep pump intakes clear; they trap fine debris as water passes through the filtering material.

Clean your pre-filters regularly to maintain effectiveness. They prevent large debris from entering the water circulation system. As pond owner, you do the actual work of emptying large debris from the pond. Pre-filters prevent fish, small animals and other large debris from entering intake pipes of external pumps.

In a small well-planted and maintained water garden, a submersible pump with a pre-filter might handle the filtration duties. Debris quantity increases in larger ponds; the burden then becomes too much for a pre-filter alone. You may combine multiple pre-filters or couple a pre-filter with an in-pond filter (performing both mechanical and biological filtering tasks). However, these systems have limits and require frequent cleaning to operate effectively.


When an ecosystem requires more than a pre-filter, skimmers get the call. Skimmers remove floating debris from the water surface and filter out large suspended particles. Available in a multitude of shapes, sizes and designs, box skimmers and floating circular skimmers are most popular. Both work by drawing water into an opening to create a laminar flow on the water’s surface. This flow brings tree leaves, un-eaten fish food, grass clippings and decaying plant material into the skimmer where a net and filter pad capture the debris.

As skimmer design evolves, manufacturers add features striving to build the ultimate pond skimmer. You can easily find a skimmer with brushes or filters to capture smaller particles instead of concentrating on large debris. New designs include UV sterilizers and clarifiers. They assist bacteria colonization (usually in the form of additional filtering material) to jump-start the biological filtration process. Manufacturers advertise skimmers capable of both mechanical and biological filtering for small water gardens.

Skimmers perform mechanical filtration that assists biological filtration elsewhere in the pond. Locating the submersible pump out of the pond and into a skimmer bars debris from the pump intake. In essence, the skimmer works as a super sized pre-filter.

Location greatly affects skimmer performance. Improperly located, a box skimmer struggles to create surface flow, especially with obstacles like plants or rocks in the path of the opening. I like to place them opposite a waterfall (or other water return) to take advantage of natural currents. Prevailing wind direction, pond shape and other factors influence skimmer location. These factors highlight the critical nature of a sound design to avoid dead spots and sharp corners that trap floating debris.

Select your skimmer with a weir (opening) relative to the dimensions of your pond. Too small an opening restricts pump flow; too large an opening produces insufficient surface flow. Most manufacturers offer multiple size weirs or an adjustable weir you can tailor to any pond. Other features include provisions for bottom drains, external pumps and automatic fill units. Choose a sturdy unit built from strong materials. Soil pressure, especially in areas with heavy clay soils or that experience freeze/thaw conditions, can easily crush a flimsy box skimmer.

Bottom Drains

Pre-filters and skimmers address large floating debris and other pump-clogging debris. However, they fail to capture all debris before arriving at the pond bottom. Bottom drains exist to accomplish this task. They act like vacuum cleaners for the pond bottom. While capable of catching large debris missed by pre-filters and skimmers, bottom drains primarily remove suspended particles.

Unlike skimmers that remove highly oxygenated top water, bottom drains remove poorly oxygenated bottom water. They draw water down through the water column, mixing the entire pond volume. This homogenizes oxygen content, moderates water temperature and creates currents for playful fish.

Although a wonderful benefit, not all pond owners trust bottom drains. Worries of leaks and clogs prevent them from installing bottom drains. Like any other component, proper installation leads to minimal mishaps. Overall, ponders encounter more leaks from waterfalls and streams than from bottom drains. Perhaps the nervousness of cutting a hole in a new liner is too much for some people to bear.

In addition, bottom drains lack any benefit in stone- and gravel-bottom ponds or in ponds without proper slope to direct debris to the drains. They are problematic in cold weather locations due to the danger of freezing, especially for ponds shut down in winter. Avoid plumbing bottom drains directly to a pump, either submersible or external.

In well-designed filtration systems, bottom drains flow into either the skimmer or a settling chamber. The most effective setups utilize gravity and water’s habit of seeking equilibrium to move pond water through the drain and into the skimmer or settling chamber. Debate continues on which way to plumb drains (skimmer vs. settling chamber). While both ways work, I favor bottom drains.

Combined with bottom drains, mechanical filtration takes a quantum leap in effectiveness. Now filtration systems can reach any debris in a pond. Ecosystems with small volumes or limited fish loads may function well with a simple skimmer/bottom drain setup. However, as volume and fish load increase, the amount of fine debris may overwhelm the skimmer (which would then pass the debris on to the biological filtration system). When conditions warrant, add a settling chamber.

Settling Chambers

Their name comes from the process used to remove suspended debris. Bottom drains feed water directly or via the skimmer into the chamber. Once in the settling chamber, debris falls out of suspension, settles to the bottom and exits by a drain. Additional filter mats and brushes help trap debris. Then the cleaned water flows into a return pipe back to the pond or continues toward biological filtration.

The vortex settling chamber uses centrifugal force to remove debris without mats or brushes. Circular movement of water within the cone chamber forces debris to fall out of suspension to the bottom. A drain allows removal of settled debris. You can plumb together a series of vortex chambers to create a gradual debris removal system. The last chamber removes the finest debris.

Pond owners contemplating settling chambers should prepare for a significant outlay of space, time and cash. Settling chambers require considerable volume (perhaps equal to 15% of total pond volume). Housing a series of chambers requires a lot of space. Plumbing complexity and maintenance increase with each chamber added.

While commercially produced chambers are expensive, the good news is that a handy pond builder can design his/her own settling chamber system. Serious koi keepers utilize a series of settling chambers. The chambers themselves are uncomplicated. Plumbing them and achieving the proper flow characteristics present a significant challenge.

Biological Filtration*

Once you have an effective mechanical system, move on to biological filtration. Sometimes the terminology seems intimidating. Once you pass nitrification, aerobic and anaerobic environments, and ion exchange, biological filtration works in a simple way. A container houses a medium that beneficial bacteria colonize. Water passes through or over the medium, bringing food to the bacteria. They “feed” on ammonia and nitrites, converting them into nitrates.

Many beginning pond owners falsely believe that clear water always equals healthy water. You cannot see the danger that lurks in your pond. Working on the unseen molecular level, biological filtration destroys harmful ammonia and nitrites to make water safe for live organisms. Signs of an effective biological filter include healthy fish, “sweet” smelling water, thriving plants and water with low levels of harmful contaminants.

Biological filters depend on an oxygen-rich environment free of sediment and debris. If sediment and debris cover bacteria colonies, they lose their oxygen and food supply, thus halting the nitrogen cycle. This illustrates the vital nature of mechanical filtration relative to pond health. Regular cleaning encourages beneficial bacteria colonies and assists in avoiding a filter “crash”. Too thorough a cleaning removes vital bacteria.

Lacking sufficient biological filtration, water quality degrades and toxin levels elevate. This creates a potentially lethal environment for fish due to oxygen deficiency and ammonia and nitrite poisoning. If toxins alone do not cause mortality, the resulting stress lowers immunity making fish susceptible to disease. Remember, clear water is not always healthy water.

Biological filters exist in all shapes, styles and designs. No “perfect” biological filter exists. Select your filter based on specific factors such as volume, fish load and pump capacity. Three basic biological filter designs prevail.

Box Filters

The simplest units, box filters, consist of a housing (the box) with filtering pads and a medium like lava rock, plastic balls or special ribbon. Water commonly moves up through the medium and then spills out of the unit back into the pond via a waterfall or stream. Filter pads help prevent debris from reaching the medium, keeping the medium cleaner and functioning properly. These filtering pads also give bacteria places to grow (when not sediment-clogged).

Box filters are the cornerstone of most water garden filtration systems. They work well despite their simplicity. They are worth every penny spent given a reasonable fish load and a good design with adequate mechanical filtration. A novice can easily set up the pump/skimmer/box filter kit most manufacturers offer.

However, box filters have limitations. The problem is not sub-par performance, but rather pond owners’ unrealistic expectations. The double whammy of heavy fish load and chronic maintenance neglect has sullied box filters’ reputation. Reasons for this could consume another article. The problem is not always the equipment, but more often how it is used.

When picking a box filter, avoid flimsy components with inferior hardware. Seek housing strong enough to withstand pressure from heavy clay soils without deforming it. Look for stainless steel screws, nuts and bolts; the plumbing bulkheads and spillway should utilize a mechanical seal to guarantee a watertight seal. I do not recommend box filters that depend on silicone sealant to prevent leaking.

Box filters should include provisions for a drain (to make cleaning easier), be easily disguised and employ effective media. With other factors equal, different media make one filter perform better than another does. Choose a medium that cleans easily, resists clogging, is relatively lightweight and has loads of surface area. Even poorly designed box filters improve significantly by replacing an obsolete medium like lava rock with a modern medium.

Bead Filters

Another type biological filter imitates the tried and true swimming pool sand filter. Water enters an enclosed housing under pressure (from the pump) that forces it through beads, plastic tubes or other material. The pressurized water agitates the medium, keeping sediment from accumulating and increasing contact between the water and the bacteria. After passing through the medium, filtered water exits and returns to the pond.

Found most often in aquaculture or as part of large koi ponds with many stages of filtration, bead filters handle higher fish loads than box filters. Costing more, they depend on well-designed and properly installed mechanical filtration to function properly. On average, they need weekly cleaning with back washing. Wastes exit via a drain.

Each manufacturer has its own take on bead filters. Ignore hype; look at construction quality and the features offered. I recommend a drain, power back washing ability and combination valving for easier operation. The type of medium plays a big role. Avoid old media like sand. Ceramic beads, plastic tubes and other patented media have taken sand’s place.

Due to their complex advanced nature, bead filters offer more surface area for bacteria than box filters. Therefore, a bead filter with the same footprint as a box filter typically outperforms it. Cleaning does not require removing beads from the unit. This minimizes disturbance of the bacteria, prevents damage from drying out and avoids exposure to tap water while cleaning.

Bead filters suffer from some of the same shortcomings as box filters. They require frequent maintenance to keep the medium clean. Large debris can clog a bead filter. Low oxygen levels can lead to the filter going anaerobic, causing a “crash”. Moreover, the plumbing knowledge to install a bead filter is complicated and they need a settling chamber. Bead filters represent a significant step up in complexity compared to box filters.

Hybrid Filters

For lack of a better term, hybrid filters represent the third style of biological filter. These filters combine mechanical filtration measured in microns along with biological filtration in one unit. Agitating their medium with an oxygen pump (instead of just passing water through them) defines next generation filters. Sometimes called a fluid bed, this environment creates ideal conditions for ammonia conversion using a very small amount of medium. Manufacturers continually introduce better next generation filters.

Bead filters depend on good mechanical filtration; next generation filters require great mechanical filtration. A little debris can clog their screens causing backups and flow problems. The fluid bed is also problematic, sometimes collapsing (falling out of suspension) which essentially stops whole process. As with bead filters, the plumbing complexity is greater and may be beyond the skills of a beginner.

The high price of next generation filters places them out of reach for most ponders. However, they clearly show where filtration is going. As technology improves and prices drop, more pond owners will employ this advanced technology.

UV Sterilizers and Clarifiers

UV sterilizers and clarifiers work with the filtration system to help control single cell algae and microorganisms. UV clarifiers kill primarily algae while sterilizers destroy bacteria, other disease-causing organisms and single cell algae.

Do not view ultra violet units as filtration units. However, when incorporated into a well-designed system, UV clarifiers and sterilizers offer increased protection against green water and fish diseases. Always follow manufacturer’s safety directions; keep them clean to maximize performance.

UV bulb effectiveness degrades over time. Replace your UV bulb yearly even if it still produces light. Avoid low wattage units except for very small water gardens. Improved designs replace glass bulbs or sleeves with acrylic or other shatterproof materials.

Natural Filtration

No article on filtration would be complete without addressing natural filtration. Consider wetlands, bogs and marshes to appreciate how well nature filters its water. The ground acts as a mechanical filter. The same bacteria found in biological filters abound in gravel streambeds, plant roots and the soil itself. Water gardeners imitate this natural filtration method with a bog or well planted stream.

I see manufactured filtration products pushing natural filtration into the background. Koi ponds typically eliminate natural elements such as aquatic plants due to the mess inquisitive koi create. Some people downplay the role of plants, especially submerged plants like anacharis, in creating well-balanced water gardens. Over-reliance on technology is shoving pond hobbyists away from what they endeavor to copy . . . a natural ecosystem.

Constant upgrades and improvements in filtration equipment highlight our evolving understanding of nature. We do know that natural systems like wetlands cleanse untold tons of water every year. These systems rely on interaction between plants, bacteria, soil and organisms to accomplish that task. By paying attention to nature’s model, our own ponds can benefit from natural filtration -- even something as simple as using a few water hyacinths.

Natural filtration in the water garden or koi pond does not have to be elaborate. Vegetative filters are widely used as a pre-filter and settling chamber combined. Root systems of plants like irises efficiently absorb nitrates and remove debris from water. Water hyacinths make extremely effective filters. Some municipalities use them to treat sewage. Submerged plants (oxygenators) excel in drawing fine sediment out of suspension and adding oxygen to the water.

Natural filtration typically entails planting a portion of the pond (or a nearby area) with bog plants. Accomplish this with an area saturated by pond water, or perhaps has a stream or other water source flowing into it. The bog provides interaction between its plants and the pond water. The plants absorb nutrients (nitrates) and capture debris. Many small water gardens use no filtration method except natural filtration.

Natural filtration is giving way to manufactured filtration systems because of maintenance and seasonality. You must prune and thin bog plants to sustain their vigor. Many aquatic plants are invasive, so bogs can quickly get out of control if left untended. Additionally, plants in non-tropical regions decline in the fall and revive in the spring. This leaves months of the year with reduced means of removing impurities from the water.


Since filtration systems represent the largest time investment pond owners make in their water garden or koi pond, many prefer cleaning a filter weekly to caring for a bog. This becomes a simple decision of economics for most owners. While this choice is understandable, ponders should consider any natural means of enhancing their pond with aquatic plants. The rewards are measurable in water quality improvements and the beauty of the plants.

In summary, filtration systems present a series of tradeoffs between time, cost and performance. If cost and space were irrelevant, the ultimate low maintenance system utilizing the latest technology would be everyone’s choice. This “perfect” system would still require maintenance; that leaves you making choices about your own filtration system.

How much work are you willing to do? How much are you willing to spend to reduce the workload? How perfect an environment do you want for your pond inhabitants?

If you grow show koi, your system will be quite different from a water garden with a few goldfish. Like all other parts of a water garden or koi pond, your overall design plan guides filtration choices. Avoid the temptation to skimp on filtration and routine maintenance. After all, it makes little sense to create a beautiful oasis for magnificent koi if you only see them when they surface to gasp for oxygen.

* Mechanical filters attract beneficial bacteria and perform some biological advantage. Biological filters strain water passing through them, contributing some mechanical filtration help. 

Introduction to this multi-part series
Your Water Garden

< Water Features, Water Gardens, and Specialized Ponds
< Planning: Location, Design, Action
< Materials and Components for your Pond
Pumps > | Lighting >

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