Bacteria convert harmful by-products from aquatic animals into less harmful nitrates. This process occurs naturally in nature's lakes and streams. In a Koi pond these bacteria are found on the walls of our ponds. They also can be found on the inside walls of the pond plumbing, attached to the skimmer basket, and on the rocks that form a waterfall.
The reason it is important to consider what filter media to use when we build biological filter systems, is to increase the available surface area for these bacteria to colonize. The important consideration is to keep the pollutants and unwanted debris out of our ponds, while keeping the beneficial bacteria in our systems.