 
Biological filtration 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.
Both of these groups of bacteria are aerobic (needing oxygen to live), sediment building up in the filter will deplete the oxygen levels so it is important to keep sediment to a minimum by having a settlement chamber first and by cleaning the filter out occasionally (but not using tap water as the chlorine will kill the bacteria).
A variety of different media are available to put in the filter, materials such as gravel, matting, hair rollers, foam, and canterbury spar are all suitable as they provide lots of surfaces for the bacteria to live on.
A biological filter will take weeks or months to mature, cultures of nitrifying bacteria are widely available and will speed up the process.
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