Biological filtration is something every koi pond requires. It is a natural process that will happen all on its own if the proper environment is provided. The basics of how biological filtration works are pretty simple, but providing the perfect environment to maximize your filters potential and provide the best water for your koi is where things get difficult.
The biofilter will grow two types of bacteria. Nitrosomonas bacteria that will oxidize ammonia into nitrite, and Nitrobacter bacteria that oxidize nitrite into nitrate. These are generally referred to as “beneficial bacteria” or “aerobic bacteria”. This bacteria will naturally form on all underwater surfaces of a koi pond assuming two main ingredients are provided, oxygen and ammonia. The ammonia is easy, the koi produce this in their waste and it will also come from decaying plant material. But oxygen isn't as easy as you might think. If the koi pond is lacking O2 then that wonderful healthy aerobic bacteria turns into anaerobic bacteria which can quickly kill your koi. For more on how to properly aerate your koi pond, please read Aeration in Koi Ponds
The basic process goes like this. 1) the koi produce ammonia. 2) the Nitrosomonas bacteria converts the ammonia into nitrites. 3) The Nitrobacter bacteria converts the nitrites into nitrates. Then 4) the nitrates are consumed by plants and algae which the koi eat and start the process all over again. Every underwater surface will grow these types of beneficial bacteria all by themselves. In nature, there is more than enough surface area to handle the amount of waste present. But in natural lakes and rivers, there are usually millions of gallons for every fish. However, in our koi ponds, we have a much higher stocking density than is found in nature so we need to provide a lot more surface area than just the sides of the koi pond. That is where you bio filter comes in.
All a biofilter does for a koi pond is provide lots of surface area to grow bacteria, that's it. Nothing magical or mysterious about it. Any surface area will do. Biofilters get fancy and expensive when they become more efficient at what they do. By this I mean they provide lots of surface area in a small space, effectively capture and remove waste and are easy to clean. Generally, the better they are at those three things, the more expensive they can get. But really it all just comes down to surface area. You will see different types of media on the market that boast a certain number of square feet of surface area for every cubic foot of media. The more sq ft they can cram into a cu ft, the better the media is and the happier your koi will be.
So back to that ideal environment, I was talking about. One thing that bacteria needs are lots of oxygen. In most cases, this can be accomplished simply by sending the water through the filter continuously. That means never turning off your pump. If you run your pump only a few hours a day to save electricity, then you deprive your bacteria of its much-needed oxygen. The bacteria will die off very quickly and turn from aerobic into anaerobic bacteria. So this causes two problems. A) the filter is no longer able to convert the ammonia produced by the koi and B) all the toxic anaerobic bacteria is flushed into the koi pond as soon as you turn the pump back on. So one crucial element for an effective and functioning biofilter is a pump that runs 24 hours a day and is turned off only when servicing the koi pond.
The next element to a well-functioning biofilter is clean media. Solid koi waste can very quickly smother and choke out all your aerobic bacteria. This will prevent the bacteria from getting its much-needed oxygen and it will again become anaerobic. This is why gravel on the bottom of the koi pond is not an effective biofilter. The waste from the koi quickly chokes out any bacteria that may have grown there. The biofilter must have some way of removing the waste produced by the koi. This is most commonly referred to as mechanical filtration. Having some sort of mechanical filtration prior to the biofilter will help greatly in keeping the media clean, the water filtered and the koi happy. Some biofilters will double as a mechanical filter using the media that provides surface area for the bacteria to also trap solid waste. Many pressurized bead filters work this way. Luckily most are very easy to clean with a backwash valve. But if you plan to use a filter like this as your primary filter then you must stay on top of the backwashing and not let the waste build up inside the media. Otherwise, the bacteria will get choked out. Some more sophisticated pond design will have elaborate prefilters before their biofilters. This way the biofilter never needs to be cleaned and the bacteria will flourish. The upfront cost of something list this is more, but it pays you back when you spend far less time cleaning the filters. A well-designed prefilter is easily cleaned out by simply opening a drain valve.
The next thing you need to consider is the amount of media you need in the filter. One square foot of surface area can handle a limited amount of waste. So you need to determine the number of koi you will have, the amount you will feed them and then make the determination on the size of the filter. It is always best to oversize your filter. The filter will not grow more bacteria then there is ammonia present in the koi pond, so just because you have a big filter, doesn't mean you have more bacteria. But by oversizing the filter, it can grow additional bacteria quickly if it is ever needed.
All koi ponds will have some amount of biological filtration even without a biofilter. But unless you have a very large koi pond and very few koi, odds are you will not have enough of the beneficial bacteria needed to convert all the ammonia produced by the koi into the end product, nitrates. So providing your koi with a filter that has a constant flow on well oxygenated, mechanically filtered water will help them live a long healthy life in your pond