Clear water does not necessarily mean clean water, it may contain colorless impurities, such as ammonia and nitrite, that are harmful and can kill Koi. Koi excrete urine and produce feces, and ammonia is excreted through the gill membranes. Also debris collects in ponds.
It is the job of the filtration system to remove waste which in the wild would be diluted by the large volumes of water or washed away by moving water.
There are three types of filtration: Mechanical, Biological and Chemical.
Mechanical pond filtration.
Most filter media have a mechanical function. Settlement chambers allow gravity to drag the solid waste out of the water by slowing the water flow. Such chambers usually come first in a filter. A vortex unit provides greater settlement, the water moves in a circular movement allowing solids to gather in the center where they can be removed. In addition to baffle plates which slow the incoming water, brushes or matting can be used to strain the water.
Biological pond filtration.
This relies on specific bacteria to break down toxic waste products to less harmful substances. There are two stages in the breakdown of ammonia, each stage involving different types of bacteria. The first stage is the breakdown of ammonia to nitrite by nitrifying bacteria, most important of which is Nitrosomonas. The second stage is the conversion of nitrite to nitrate by Nitrobacter.
Activated carbon removes ammonia and other organic waste products by adsorption, this means that the waste substances become linked to the surface of the carbon. When the surface is 'full up' it has to be replaced.
Zeolite removes ammonia and nitrite from the water. A good feature of Zeolite is that it can be cleaned by soaking in salt water (6g per litter) for 24 hours and then reused.
If a large biological filter is present chemical filtration should not be needed, but it is good to use while the biological filter is maturing or isn't big enough for the pond.
Sand (Glass) filter. Some Koi keepers use a sand, or glass, filter as a final stage to 'polish' the water. The water is passed under high pressure through sand and comes out very clear, bacterial activity also takes place in the sand filter. Sand filters are expensive though, and you can't make one yourself because of the high pressure involved.