The use of biofilters is common in closed aquaculture systems, such as recirculating aquaculture systems (RAS). The biofiltration techniques used in aquaculture can be separated into three categories: biological, physical, and chemical. The main biological method is nitrification, physical methods include mechanical techniques and sedimentation, and chemical methods are usually used in tandem with one of the other methods. Some farms use seaweed, such as those from the genera Ulva, to take excess nutrients out of the water and release oxygen into the ecosystem in a “recirculation system” while also serving as a source of income when they sell the seaweed for safe human consumption.
Many designs are used, with different benefits and drawbacks, however the function is the same: reducing water exchanges by converting ammonia to nitrate.  Ammonia (NH and NH) originates from the brachial excretion from the gills of aquatic animals and from the decomposition of organic matter.  As ammonia-N is highly toxic, this is converted to a less toxic form of nitrite (by Nitrosomonas sp.) and then to an even less toxic form of nitrate (by Nitrobacter sp.).  This "nitrification" process requires oxygen (aerobic conditions), without which the biofilter can crash.  Furthermore, as this nitrification cycle produces H, the pH can decrease which necessitates the use of buffers such as lime.