Outside filters generally take the form of boxlike structures that hang onto the back or side of the aquarium or canisters that rest on the floor below. Water is drawn via an internal motor through a series of filter mediums. In the process, it undergoes biological, chemical, and mechanical filtration. The mechanical filtration — that is, the removal of large particles — is carried out by a number of porous materials such as filter pads, floss, or various cartridges. This is the first step in the filtering process. After this, the water is propelled through activated carbon or other materials that serve as chemical filters. The flow of oxygenated water through the filter material allows for the growth of beneficial aerobic bacteria, thereby providing biological filtration (the breakdown of ammonia to nitrates and nitrates). As mentioned earlier, it is important to replace the chemical filter materials regularly so that harmful chemicals do not leach back into the aquarium. Likewise, the mechanical aspects of the filter must be kept clean so that water can flow throughout the entire system. If blockages develop, the beneficial aerobic bacteria will perish. This interrupts filtration and, if it occurs on a large scale, can quickly raise the ammonia content of the water to dangerous levels. The outflow of water back into the aquarium disturbs the surface and allows for the oxygenation of the water by mixing it with atmospheric oxygen. Most of the newer models of outside filters have diffusers or other means of regulating the outflow of water or directing it to certain areas of the aquarium. This is useful in creating currents that will disturb otherwise neglected areas of the tank, keeping sediments afloat where they can be collected by the filter's intake system.

When cleaning filters, it is important to retain some of the old filter material, and to add this to the new when the filter is refilled. The beneficial bacteria contained on the old material will reproduce rapidly and increase the filter's effectiveness. Also, when cleaning the filter box itself, use temperate as opposed to hot water, so as not to kill the bacteria that have become established on the inner surfaces of the filter.