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Fish anatomy

Fish are a diverse group of vertebrate animals that have gills and live in water. A typical fish uses gills to obtain oxygen from the water, while at the same time releasing carbon dioxide and metabolic wastes (Figure 7.2). The typical fish is ectothermic, or cold-blooded, meaning that its body temperature fluctuates according to the water temperature. Fish have almost the same organs as terrestrial animals; however, they also possess a swim bladder. Positioned in the abdomen, this is a vesicle containing air that keeps the animal neutrally buoyant in the water. Most fish use fins for movement and have a streamlined body for navigating through water. Often, their skin is covered with protective scales. Most fish lay eggs. Fish have well-developed sensory organs allowing them to see, taste, hear, smell and touch. In addition, most fish have lateral lines, which sense pressure differences in the water. Some groups can even detect electrical fields, such as those created by heartbeats of prey species. However, their central nervous system is not as well developed as in birds or mammals.

Main external anatomical features

Eyes - Fish eyes are very similar to those of terrestrial animals, such as birds and mammals, except their lenses are more spherical. Some fish, such as trout and tilapia, rely on sight to find prey while other species use mainly their sense of smell.

Scales - Scales provide protection for the fish by acting as a shield against predators, parasites, diseases and physical abrasion.

Mouth and jaws - Fish ingest food through the mouth and break it down in the gullet. Often, the mouth is relatively large, allowing the ingestion of substantial prey. Some fish have teeth, including sometimes on the tongue. Fish breathe by bringing water in through the mouth and expelling it through the operculum.

Gill cover/operculum - This is the external covering of the gills, which offers protection to these delicate organs. It is often a bony plate and can be seen opening and closing while the fish is breathing.

Vent - This is the external opening on the bottom of the body near the tail. Solid wastes and urine pass through the digestive track, through the anus, and are expelled through the vent. In addition, the vent is where reproductive gametes (sperm and eggs) are released. The vent has a similar function to a cloaca.

Fins - Paired fins, both the pectoral fins and pelvic fins, are located on the bottom of the fish body. They provide manoeuvrability and steering control. Odd fins, the dorsal fins and anal fins can be found on the top and bottom of the body and provide balance and stability as well as steering control. The tail fin is at the opposite end from the head and provides the main propulsion and movement for the fish. Fins often have sharp spines, sometimes with attached poison sacs, that are used for defence.


Fish breathe oxygen using their gills, which are located in each side of the head area. Gills consist of structures called filaments. Each filament contains a blood vessel network that provides a large surface area for the exchange of oxygen and carbon dioxide. Fish exchange gases by pulling oxygen-rich water through their mouths and pumping it over their gills, releasing carbon dioxide at the same time. In their natural habitat, oxygen is supplied either by aquatic plants that produce oxygen through photosynthesis or from water movements such as waves and wind that dissolve atmospheric oxygen into the water. Without adequate DO, most fish suffocate and die. That is why adequate aeration is so crucial to successful aquaculture. However, some fish are equipped with an air breathing organ, similar to lungs, that allows them to breathe out of water. Clariidae catfish are one such group of fish that are important in aquaculture.


Nitrogen wastes are created as fish digest and metabolize their feed. These wastes come from the breaking down of proteins and the reuse of the resulting amino acids. These nitrogenous wastes are toxic to the body and need to be excreted. Fish release these wastes in three ways. First, ammonia diffuses into the water from the gills. If ammonia levels are high in the surrounding water, the ammonia does not diffuse as readily, which can lead to ammonia accumulation in the blood and damage to internal organs. Second, fish produce large quantities of very dilute urine that is expelled through their vents. Some nitrogen (proteins, amino acids, ammonia) is also present in the solid wastes that are expelled through the vent. Fish use kidneys to filter their blood and concentrate the waste for disposal. The excretion of urine is an osmotic regulation process, helping fish to maintain their salt content. Freshwater fish do not need to drink, and in fact need to actively expel water to maintain physiologic balance.

Fish reproduction and life cycle

Almost all fish lay eggs that develop outside of the mother's body; indeed, 97 percent of all known fish are oviparous. Fertilization of the eggs by the sperm, known as milt in fish biology, also occurs externally in most cases. Male and female fish both release their sex cells into the water. Some species maintain nests and provide parental care and protection of the eggs, but most species do not attend the fertilized eggs which simply disperse into the water column. Tilapias are one example of fish that have extensive parental care, taking the time to maintain nests and actually brood the young fry in the mouth of the females. The reproductive organs of fish include testes, which make sperm, and ovaries, which make eggs. Some fish are hermaphrodites, having both testes and ovaries, either simultaneously, or at different phases in their life cycle.

For the purposes of this publication, an average fish will pass through the life stages of egg, larvae, fry, fingerling, grow-out (adult fish) and sexual maturity (Figure 7.3). The duration of each of these stages is dependent on the species. The egg stage is often fairly brief and usually depends on water temperature. During this stage, the eggs are delicate and sensitive to physical damage. In culture conditions, the water needs to have adequate DO, but the aeration must be gentle. Sterile procedures and good hatchery practices prevent bacterial and fungal diseases of unhatched eggs. Once hatched, the young fish are called larvae. These small fish are usually poorly formed, carry a large yolk sac, and are often very different in appearance from juvenile and adult fish. The yolk sac is used for nourishment, and it is absorbed throughout the larval stage, which is also fairly short depending on temperature. At the end of the larval stage, when the yolk sac is absorbed and the young fish begin to swim more actively and move to the fry stage.

At the fry and fingerling stage, fish begin to eat solid food. In the wild, this food is generally plankton found in the water column and algae from the substrate. During these stages, fish are voracious eaters, eating about 10 percent of their body weight per day. As the fish continue to grow, the percentage body weight of food per day decreases. The exact demarcations between fry, fingerlings and adult fish differ between species and between farmers. Generally, fry, fingerlings and juvenile fish need to be kept separate to prevent the larger fish from eating the smaller individuals. The grow-out stage is the stage that aquaponics typically focuses on because this is when the fish are eating, growing and excreting wastes for the plants. Most fish are harvested during the grow-out stage. If fish are allowed to grow past this stage, they begin to reach sexual maturity, where their physical growth slows down as the fish devote more energy into the development of sex organs. Some mature fish need to be kept to complete the cycle during breeding operations, and these fish are often referred to as broodstock. Tilapias are exceptionally easy breeders, and can in fact breed too much for a small-scale system. Catfish, carp and trout require more careful management, and it may be better to source fish from a reputable supplier. It is outside the scope of this publication to detail aquaculture breeding techniques, but please refer to the section on Further Reading for helpful sources.

Source: Food and Agriculture Organization of the United Nations, 2014, Christopher Somerville, Moti Cohen, Edoardo Pantanella, Austin Stankus and Alessandro Lovatelli, Small-scale aquaponic food production, Reproduced with permission.

Food and Agriculture Organization of the United Nations

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