If you are setting up an indoor aquarium for the first time, a filtration device is one of the most important pieces of equipment you will purchase. Filters are needed for both freshwater and marine (saltwater) ecosystems; they remove physical and chemical waste from the water. Because an aquarium is an enclosed environment, these waste products and harmful chemicals have no means of natural dispersion, and thus must be physically removed. Filters are critical in supporting the life systems in your aquarium, whether fish, plants, or invertebrates.

Decomposing organic matter, including excreta from fish, produce ammonia, which is toxic to fish. In the natural world, ammonia is oxidized into nitrites through bacterial processes; nitrites are then further oxidized into much less toxic nitrates, which in turn naturally fertilize marine plant life. Because most aquariums have unnaturally large concentrations of fish, however, excessive amounts of ammonia are routinely produced, and the accumulation of toxic ammonia in aquariums is the biggest cause of fish mortality in these closed environments.

There are three basic methods of aquarium filtration: biological, mechanical, and chemical. Biological filtration attempts to most closely recreate what happens in the natural world; these filters promote the growth of bacteria that propel the oxidation process forward. A basic biological filter may simply be a chemically inert, porous sponge, which provides an enlarged surface area for colonies of bacteria to develop. Initially, it make take several weeks for the colonies to form, leaving an aquarium vulnerable to ammonia buildup in the meantime. If a tank is stocked with fish too quickly, it may suffer from “new tank syndrome,” in which the propagation of bacteria cannot initially keep up with the production of ammonia, and fish will fall ill or die.

One popular biological filter is an “undergravel filter”: a porous plate that is laid underneath the substrate in your aquarium, with one or more uplift tubes. Air stones placed under the uplift tubes force water out, creating negative pressure underneath the filter plate. Water then percolates downward through the substrate layer, which is colonized by bacteria and thus acts as the filtration material. A water pump can accelerate the filtration process. However, such filters may not work with fine substrates such as sand or peat; gravel works better. Also, the substrate layer must be level, to ensure even water flow through the entire substrate; if you plan to keep marine animals that dig into the substrate layer, an undergravel filter may not be suitable.
Another type of biological filtration system is the trickle filter, or “wet-dry filter.” Normally, these filters are placed above the aquarium. Water is pumped over a series of perforated trays containing filter wool, or another filter material. As water trickles through the trays, the filter wool is kept wet but not submerged, encouraging the growth of aerobic bacteria colonies that oxidize the ammonia in the water. The water drips back down into the tank once it has passed through the trays.

Mechanical filtration physically removes particulate material from the water; this is achieved by passing the water through a sieve, trapping uneaten food, excreta, plant debris, and other waste matter. This solid waste must be removed from the filter on a regular basis (weekly), before it can decay and dissolve back into your tank. The most common form of mechanical filtration is through a canister filter, which usually hangs on the back of the tank. Water is pumped in, passed through whatever filter material is used, and then pumped back into the tank. These filters are able to process large quantities of water quickly, and they are easy to remove and clean. However, mechanical filtration through a canister does not remove dissolved ammonia, microscopic bacteria or algae, or solids trapped by gravel, plants, or aquarium decorations.

A protein skimmer is the best form of mechanical filtration for a saltwater tank. The motion created by the skimmer injects air bubbles into the tank, creating a foam similar to sea foam. Organic molecules collect in this foam, which is captured in a collection cup. This method of filtration removes dissolved organic compounds before they break down into ammonia and nitrites.

Chemical filtration aims to remove dissolved wastes from your tank’s water. To some extent, the marine plants in your tank extract dissolved waste from the water as they grow, acting as natural filters. Chemical filtration methods, most commonly using activated carbon, aid in this effort. The carbon’s microporous structure absorbs dissolved organic materials, toxic metals and gasses, growth-inhibiting enzymes, and other harmful elements. The carbon should be positioned in the tank such that water passes through it, not just over it; the carbon also needs to be replaced periodically.

There are various other substances that you can introduce into your tank to remove specific resins or minerals, if you experience a buildup of some undesirable element. Various treated sponges can remove phosphates, nitrates, and other minerals. You would need to test your water to determine if it contains excessive amounts of any harmful materials.

Your choice of filter will depend on what kind of ecosystem you are creating in your aquarium; you may need to employ a variety of filtration devices to ensure a clean and healthy environment for your fish and plant life.