Choosing the correct pond filter media is essential to maintaining a healthy Koi pond. Fish excrete urea, which becomes ammonia. Ammonia is oxidized first into nitrite and then into nitrate by bacteria in the water. Ammonia and nitrite are toxic to fish; nitrate is relatively harmless and is taken up by aquatic plants as a nutrient.

Nitrifying bacteria exist on every surface in a pond but can only convert the ammonia and nitrite that they physically contact into harmless nitrate. Biological pond filters contain media that provides a substrate upon which colonies of nitrifying bacteria can be concentrated. The entire volume of the pond is circulated through the biological filter once every 60 to 90 minutes, forcing all of the ammonia and nitrite in the water into contact with the bacteria.

These bacterial colonies live on surfaces. While they will colonize smooth surfaces, such as marbles or pebbles, they cling better to irregular and ridged surfaces. Filter media with higher surface areas support higher populations of beneficial bacteria per volume of media. Small straw-like structures or blocks of sponge, for example, would support more bacterial growth than small rods or a solid block, because the straws and sponge provide both inner and outer surfaces on which the bacteria can grow.

Gravel, rocks, engineered ceramics and zeolites are common pond filter media and have been used for decades. Engineered plastic designs, however, are far more popular now. Artificial media is lightweight, stable, and designed to have extremely high surface areas. Bio balls are highly efficient filter media. They are plastic spheres with hundreds of tiny rods extending from the surface of the ball. These rods drastically increase the surface area of bio ball when compared to a smooth ball of the same size. Polymer ribbons with embossed ridges and grid patterns are also highly effective media in biological pond filters. The ribbon is unspooled into the filter container and allows good water flow, while the embossed ridges on the ribbon increase the surface area for the bacteria to colonize by a factor of ten or more. Savio Springflo is a good example of ribbon-like Koi pond filter media.

Some biological pond filters contain media in the form of fibrous mats or pads. These mats vary in density, which impacts the flow characteristics of the pond water being filtered. Course filters mats allow a high flow rate and filter out large debris. Finer filters have higher densities and much more surface area per cubic inch, but tend to impede flow and require greater head pressure to move water through the filter. They also tend to become blinded by small particulate matter more quickly than less dense media. Most filter designs pass water first through a course, less dense media, then through successively more dense media in order to prevent blinding of the fine mats.

Unfortunately, the nitrogen cycle is not perfect. Bacteria die and fall off the media, and clumps of bacterial colonies are sometimes dislodged and swept away in the water flow. Over time these materials accumulate and clog the filter. In order to maintain good water flow over healthy bacterial colonies, the filter media requires periodic cleaning. This is typically accomplished by back-flushing the filter to an area outside of the pond.

Chemical cleaners or chlorinated water should NEVER be introduced into the filter media; doing so will kill the bacteria and also add the toxic chemicals or chlorine into the pond water. The goal of cleaning biological filter media is removal of dead bacteria and sludge buildup. A healthy coating of nitrifying bacteria must remain on the media or it will not be able to remove ammonia and nitrite from the pond water.