Usually designed as external canisters with strong motors, diatom filters utilize the fossilized remains of tiny organisms, known as diatoms, as a filter medium. This medium is referred to as diatomaceous earth. The unit's motor forces water through the diatomaceous earth at a high rate, removing even the tiniest bits of suspended matter. Water leaving the filter is exceptionally clear. Most diatomaceous earth filters are equipped with powerful motors that allow for a rapid turnover of aquarium water. This, combined with the extreme effectiveness of the filtration provided, leads many to use such filters on an occasional basis only. Their only drawback is that they clog quickly, because so much material is removed in a very short time.

Most diatom filters are equipped with a reverse flush, which is a system that allows for easy cleaning of the unit. Even so, they generally should not be utilized for long periods of time, especially if they can't be regularly monitored. Diatom filters are, however, useful adjuncts to any filtration system, especially in large aquariums, and are indispensable during emergencies.