Each method of filtration fulfills a specific role, although there is some overlap among them. Of the three types of filtration, biological filtration is by far the most important. If this aspect of the filtration system is not working effectively it will be nearly impossible to keep any but the very hardiest of fish or invertebrates alive. Basically, biological filtration is closely linked to the nitrogen cycle, which is the process through which ammonia and other nitrogenous compounds are rendered less toxic through the action of nitrogenous bacteria (as explained in detail in Chapter 2). Some degree of biological filtration may be achieved with nearly any filter, and several types, such as fluidized bed filters and trickle filters, utilize this method of filtration nearly exclusively.

Mechanical filtration refers to the physical removal of suspended materials from the water. This is accomplished by using a mechanical pump to move the water through materials such as filter floss, pads, or sand. These materials act to trap the suspended particles and must, of course, be periodically rinsed so that they can function at full capacity. Outside and box filters are the best mechanical filters, but nearly all filters perform some degree of particulate removal.

The removal of proteins and other dissolved organic materials from aquarium water is accomplished using chemical filtration. Such materials impart a yellowish tinge to the water, and their presence creates an unhealthy environment for aquatic animals. A variety of materials have chemical filtration potential. Perhaps the most common is activated carbon, which is extremely effective at maintaining water clarity. Other commercially available products can be utilized to remove ammonia and nitrates from the water. Box filters, outside filters, and most others can accommodate various chemical filtration substances.