Although often viewed as primitive by modern-day hobbyists, box filters have much value and should be considered in certain circumstances. Box filters sit within the aquarium, on the bottom, and are powered by a motorized air pump. Filter floss, or a porous filter pad, functions as the mechanical stage of filtration, while activated carbon or other materials can be used to chemically filter the water. Nitrifying bacteria develop on the filter floss and other filter materials, allowing for effective biological filtration.

Most box filters that are currently available are fairly small, a fact that limits their use to specific situations. Also, because they sit within the aquarium, such filters do detract from the aquarium's overall appearance. Box filters are, however, very useful in quarantine aquariums. In these situations, aesthetic considerations do not matter as much as does function, and these simple filters are easily cleaned. Another useful aspect is that airflow from the pump to the filter can easily be controlled by the use of a mechanical gang valve. This allows you to control the flow rate of the water and air leaving the filter. This is especially useful in situations where you are raising small fish fry or other delicate creatures that will be disturbed by strong currents. Also, because the current is directed upward, large portions of the aquarium water will remain undisturbed and calm.