Biological Filtration is the removal of nitrogen breakdown by-products (Ammonia, Nitrite, Nitrates, etc.) from the aquarium water through the use of bacteria.

Nitrogen compounds appear as a result of animals and food being added to the tank, algae dying within the tank, and the respiration and metabolism of the fish and invertebrates in the tank. The water quality of your aquarium will start to deteriorate quickly with the addition of more animals; however, biological filters can counteract this negative effect by removing the organically produced toxic compounds. Biological filtration is often executed with live rock, live sand, or bio-balls placed in a wet-dry filter.

Biological filtration is used to (1) remove nitrogen breakdown by-products, (2) convert ammonia to nitrite, (3) convert nitrite to nitrate, and (4) remove some nitrate from the system. To do this, bacteria is used to eliminate ammonia, nitrite and nitrates. Ammonia is broken down to nitrite by a form of bacteria known as Nitrosomonas. These bacteria can appear spontaneously or proliferate when adding/transferring gravel or rock. Ammonia tests should always show zero ppm; even small amounts of ammonia are unacceptable in reef systems because they will easily harm your aquarium’s inhabitants.

Nitrobacter bacteria also appear spontaneously in aquariums and convert the nitrite to nitrate, a less damaging compound. If nitrite tests show the mere presence of nitrite, your tank must be thoroughly cleaned. You’ll have to remove any sitting organic matter and dead or dying algae. You’ll need to flush the mechanical filters, sift the gravel, check the corner overflow boxes and skimming siphons, etc. The presence of nitrite may be directly related to the presence of too much fish food or the tank being overloaded with life forms. Whatever the reason, your filters aren’t being able to efficiently deal with the biological load present in your aquarium. In accordance to the cause, you may have to remove life forms or add additional biological filtration.

Nitrates are different than ammonia and nitrite. Nitrate is not notably harmful to all-fish aquariums, but it is to reef aquariums. Nitrates directly affect the well-being and aesthetics of corals and other invertebrates. When testing your nitrate level, the lower the better; anything under 10ppm is satisfactory but in very sensitive reef aquarium a level of 1-4ppm is desirable.