Ammonia (NH₃) is a waste product excreted by fish and the decomposition of uneaten food. NH₃ is toxic to fish and must be continuously filtered out of a closed system like an aquarium. Fortunately, microorganisms called nitrifying bacteria can consume NH₃ as their source of energy, eventually converting it to a non-toxic substance called nitrate (NO₃).

This set of illustrations depicts three different designs for aerobic biological filtration of nitrogenous waste in aquariums. Water passes through a high surface area medium (ie: gravel, bio ball, or sponge) that permits colonization of nitrifying bacteria. Oxygen is diffused into the water by either agitation (biotower filter) or pumping room air through an air stone (under gravel or sponge filter).