The substrate of an aquarium refers to the material used on the tank bottom. It can affect water chemistry, filtration, and the well-being of the aquarium's inhabitants, and is also an important part of the aquarium's aesthetic appeal. The appropriate substrate depends on the type of aquarium; the most important parameter is whether the aquarium contains fresh water or saltwater.
Substrates for freshwater aquaria
For freshwater aquaria, gravel is the most common substrate. Gravel sold specifically for use in aquaria is chemically inert. It may be naturally colored or dyed, and may have a polymer seal to ensure it does not affect water chemistry.
Types of substrates for freshwater include the following:
- Gravel. Aquarium gravel can be as coarse as pea-sized or as fine as 1–2 mm. It is commonly composed of quartz or other lime-free minerals. 
- Shell grit, crushed limestone, crushed marble or crushed coral skeletons. Because calcium carbonate, the primary component of these substrates, increases water hardness and pH, it is used most often for particularly for hard water species, such as those for African rift lake cichlids or cichlids from Central America. Calcium carbonate substrates are poorly suited to aquaria housing most other freshwater aquarium fish, particularly river species, which are adapted to soft water. 
- Peat, or decomposed plant matter. Peat is used most commonly in soft water or blackwater river systems, such as those mimicking the Amazon River basin. In addition to being soft in texture and therefore suitable for demersal (bottom-dwelling) species such as Corydoras catfish, peat is reported to have a number of other beneficial functions in freshwater aquaria. It softens water by acting as an ion exchanger, it contains substances good for plants and for the reproductive health of fishes, and can even prevent algae growth and kill microorganisms. Peat often stains the water yellow or brown due to the leaching of tannins. 
- Sand. This is often recommended for use with certain species, such as the river stingrays of family Potamotrygonidae, which bury themselves in the fine substrate. However, these species can be successfully kept with coarser substrates as well.
In some aquaria, different substrates are used in different parts of the tank. For example, peat can be used in one corner, while gravel in another portion allows rooted plants. 
Freshwater aquaria with live plants
Planted tanks require a substrate that will remain loose enough for plant roots to penetrate it. The substrate should be chemically inert and free of sharp edges. Examples include sand and gravel; fine gravel (1–2 mm) is preferred by some aquarists because coarser substrates allow debris to settle within the gaps between grains, which is particularly difficult to clean in a planted aquarium. Sloping the substrate so it is most shallow in front accommodates larger plants with correspondingly larger root systems in the back. The substrate for plants should be at least 5 cm (2 in) deep. Often, a lower layer of richer substrate such as potting soil, peat, vermiculite, or certain types of clay are used as a source of iron and trace elements for plant roots.
Substrates for saltwater aquaria
For saltwater aquaria, coral gravel and coral sand are most common. Composed primarily of calcium carbonate, coral skeletons have a buffering effect on the water's pH. They also contribute calcium, needed by some invertebrates, to the water.
In a reef aquarium, the substrate can be an important part of managing the water chemistry. Calcium carbonate substrates such as those made from coral or oolitic aragonite are commonly used; when these minerals, insoluble in water, are dissolved by acid secretions, they release calcium and strontium, both of which are important to invertebrates such as stony corals.
Coral sand is considered the best substrate for a reef aquarium. At a depth of about 2.5 cm (1 in), it allows anoxic zones to form and host anaerobic bacteria which in turn denitrify the water, that is, convert nitrate to nitrogen gas. Animals such as sleeper gobies and some invertebrates such as turbo snails are useful to stir the sand.
Aquaria with marine invertebrates often incorporate live rock, which can be considered part of the substrate. Made of calcium carbonate, it has the same effects on water chemistry as coral gravel and sand. It is riddled with small holes and cavities which allow anoxic zones to form.
Substrates for specialty tanks
In breeding tanks for egg-scattering species, a layer of marbles is sometimes used as a substrate, allowing the eggs to fall into the gaps between the marbles where the parents cannot eat them.
Quarantine tanks (sometimes called hospital tanks) often use no substrate at all. This assists in keeping the aquarium as clean as possible. 
Biological filtration via substrate
Beneficial bacteria colonize all aquarium surfaces that are exposed to aerated water. Because the numerous particles have a high surface area, substrates are often employed in biological filtration.
In an undergravel filter, substrate (most commonly gravel or crushed coral) is placed on top of a grate containing one or more uplift tubes. Water is pumped up the tubes using either an air pump or small water pump, forcing flow through the substrate and aerating the entire gravel bed. Beneficial bacteria colonize the gravel bed and provide biological filtration. Undergravel filters are most often used in small aquaria, although they can be used in larger systems.
Undergravel filters are not effective if the substrate bed is uneven or if very fine substrates such as sand or peat are used. In an uneven gravel bed, water will flow only through the thin portions of the bed, leaving the more heavily covered areas to become anoxic. Because of this, animals that dig, such as cichlids, are best kept in an aquarium using some other type of filtration.
Even without an undergravel filter, some nitrifying bacteria are present on the surface of the substrate.
- ^ a b Substrate Materials. The Tropical Tank. Retrieved on 2006-05-02.
- ^ a b c d e Scheurmann, Ines (1985). Natural Aquarium Handbook, The, (trans. for Barron's Educational Series, Hauppauge, New York: 2000), Munich, Germany: Gräfe & Unzer GmbH.
- ^ Randall, Karen. A Look At Substrate. The Krib. Retrieved on 2006-06-08.
- ^ Delbeek, J. Charles, Julian Sprung (1994). Reef Aquarium, The, Volume 1. Coconut Grove, Florida: Ricordea Publishing.
- ^ S. Russell. Breeding Zebrafish (Chapter 2). The Zebrafish Book. Retrieved on 2006-05-02.