As the biological processes within an aquarium take place, fish and nitrifying bacteria utilise oxygen and waste gases such as carbon dioxide and nitrogen are produced. If an imbalance of harmful gasses occurs, and the oxygen content in the water becomes deficient, the fish will literally suffocate. An indication of this happening is when fish hang just below the water surface and gulp air directly from the atmosphere. (Note: some fish such as labyrinth fish and Corydoras sp. will occasionally take air from the surface naturally).

In an aquarium, the only place that an exchange of gases can occur is where water is in direct contact with the atmosphere. It is therefore important to maximise the surface area of the water.

Tall tanks may not have a large enough surface area to provide an adequate oxygen interchange and in heavily stocked aquariums the demand for oxygen by the fish may exceed the supply at the surface. In very warm tanks oxygen diffuses rapidly from the water and additional agitation of the water surface will be required to maximise the surface area available for the exchange of gases.

Normally the return from a filter agitates and circulates the water enough to promote sufficient diffusion of gasses in and out of the water and additional aeration is not necessary. To address any additional aeration requirements, an airpump is sometimes employed. The stream of pretty bubbles which it produces, via an air stone, is often mistakenly thought to somehow inject air into the water but in fact an airpump actually provides aeration by circulating and disturbing the water surface to create a larger area for oxygen exchange. Too much turbulence at the water surface may drive off carbonic acid, which is an important plant fertilizer or cause too great a current for the fish. It is for these reasons that airpumps and filters are available in a range of sizes or have flow regulators to tailor their output to the tanks needs.