The biofilter's job is to detoxify waste products such as ammonia, nitrite and some phosphate. These invisible waste products can weaken or kill your koi and also act as fertilizer which creates algae problems. Good bacteria, called nitrifying bacteria, attach themselves to the biofilter material (media) and break down these waste products. Good flow through the biofilter must be maintained. The bacteria require good flow of oxygenated water to function properly. Bacteria are slow growers and if left undisturbed will colonize more completely and quickly. Many species of bacteria are responsible for complete biofiltration. Biofiltration also includes the decomposition of organic wastes like starches and fats. Clear water is dependent on a complete population of many types of bacteria. Constant cleaning of a biofilter sill simply wash away the beneficial populations of bacteria. The biofilter will function extremely well if most of the solids have already been removed by a good mechanical filter. Backwashing will be minimized due to lack of solids.
Bacteria will grow the fastest in warm water. The summer is a good time of year to clean the biofilter because the bacteria can grow back quickly. When temperatures are below 60 degrees F, cleaning should be minimal if at all.
An important design aspect to the biofilter is the manner in which the media is contained within the filter tank. The media should be supported on a strong grate above an intake manifold to ensure adequate flow of water through the media. 6" to 12" of water above and below the media will help in the even distribution of water flow.
Bacteria will grow on almost anything inert. The hobbyist can choose from a wide range of medias to use in the biofilter. Gravel is cheap and does provide a fair growing site for nitrifying bacteria. Gravel also provides the correct environment for the "algae lysing" type of bacteria. I have used this phrase for lack of a better word. In theory these bacteria are responsible for a pond's ability to clear itself of "pea soup" algae. However, gravel can plug up quickly because it is heavy. Gravel should be evenly graded and sized so that small gravel grains do not plug up water passage ways. One big drawback to gravel is it's tendency to trickle around the support grate and end up at the bottom of your filter, clogging pipes and creating stagnant piles of sludge. The support grate and any screening should be made to fit very tightly inside the filter tank to prevent this problem.
Synthetic medias don't have a lot of the problems inherent to gravel. Being lightweight and less clogging makes synthetic medias easier to handle and clean. Most of the synthetics have a large surface area per cubic foot for growing bacteria. This attribute gives a bigger biofilter in a smaller space. However synthetic medias may not grow the "algae lysing" type of bacteria very easily. The "algae lysing" bacteria grow better in slightly stagnant and low oxygen zones. Synthetics are usually very free flowing. Be careful when backwashing synthetic medias because they can clean to easily and might wash away too much bacteria. Examples of proven useful synthetic bio-medias are: open cell foam, polymat, bioballs, bio bale, and filter brushes.