The Marketplace is now widely available! Install insights today.
Download AppBlogFeaturesPricingSupportSign In

The main idea of this section is to introduce several important anatomical features of fish and to relate them to function and physiology. There are more than 20,000 species of freshwater and marine fish on our planet, each with specific requirements and ecological niches, which has led to specific body adaptations. However, many of the fish, especially teleosts (bony fish with a moveable pre-maxilla), share some common features. Although the number of species used in aquaculture is probably over 200, the number used in aquaponics is narrower, and mostly restricted to freshwater fish (Table 1).

Table 1: Summary of the species of fish used in aquaponics, including those cited in two international surveys on aquaponic practitioners

(Love et al. 2014; Villarroel et al. 2016)

Common nameSpeciesFamilyOrderTilapiaOreochromis niloticusCichlidaeCichliformesCatfishPangasius pangasiusPangasiidaeSiluriformesKoiCyprinus carpioCyprinidaeCypriniformesTroutOncorhynchus mykissSalmonidaeSalmoniformesBassMorone saxatilisMoronidaePerciformesPerchSander luciopercaPercidaePerciformesBlue gillLepomis macrochirusCentrarchidaePerciformes

Most of the fish used in aquaponics follow a basic anatomical outline (Figure 1). Looked at longwise, there are three main regions of the body: the head, the trunk region, and the tail (Canada Department of Fisheries and Oceans 2004). In terms of possible abnormalities, veterinarians tend to focus on problems related to the eyes, fins and skin. Apart from those, there are other parts of the external anatomy that are important in terms of indirect measures of fish welfare, fish quality, and health problems, and one should be able to locate these. For example, blood sampling usually involves injecting a needle underneath the lateral line in the tail region to find the caudal vein. To tag individuals, passive integrated transponder tags (PIT tags) are normally injected into the muscle under the dorsal fin. Some other plastic paints can be injected on or near the mouth and eyes, but any type of exterior tags often cause problems since they affect the very delicate skin and can cause infections. If nothing else, basic knowledge of some species-specific anatomy can also help to avoid fish fraud when purchasing them commercially.

Eyes and nose

As opposed to some cartoon characters, real fish have no eyelids. Thus, not only are their eyes in direct contact with the surrounding water at all times, giving an idea of the importance of water quality, they are also quite light sensitive (they have no way of ‘closing’ their eyes). This is why many fish prefer to avoid direct sunlight and congregate in locations with shade. The Mexican cavefish

(Astyanax mexicanus) is one example of a blind fish, but most fish used in aquaponics can see very well. While alive, bilateral exophthalmia (the bulging of both eyes from their sockets) is often used as a general indicator of infection. Unilateral exophthalmia is probably the result of a contusion. After slaughter, the whiteness of the eye is used as a quality indicator (see Council Regulation (EC) 2406/96). For example, a high-grade fish will have a convex eye with a black and shiny pupil, while fish with a concave eye, grey pupil, and a ‘milky’ cornea should be discarded. Close to the eyes are two small openings (nares) which lead to an area with olfactory sensors which can be quite sensitive in many fish. For example, salmonids use their olfactory sensors during migration in order to return to their original breeding grounds. Technically, in order to be able to smell anything, a current has to be established in and out of the nares, normally while fish are swimming but, unlike in mammals, the holes do not lead to the throat.


Figure 1: Basic external anatomy of a fish (from

Opercula and gills

The operculum is a bony cover that shields the gills, the lungs of the fish which capture the rather limited supply of oxygen dissolved in water. The opercular frequency, or the rate at which the opercula open and close over a period of time, can be used to verify whether fish are breathing correctly or may be overly stressed. In anesthetized or dead fish, veterinarians often ‘check under the hood’ by lifting up the opercula to examine the gills, which should be bright red and moist, and not covered in mucus, white, or smelly. External observation of the gills can also provide information about possible bacterial or parasitic infections. Compared to mammals, fish gills are thus more of an external organ than an internal one, again underlining the importance of water quality to protect this delicate and important organ (e.g. correct water pH). Finally, apart from oxygen absorption and CO2 release, the gills are an important outlet for nitrogenous waste (Figure 2). Hoar & Randall (1984) calculated that more than 80% of ammonia (NH3) is excreted via the gills, while only trace amounts are passed as urine.


Figure 2: The gills work according to the counter flow principle: water and blood flow in opposite directions.

The O2 content in blood can therefore rise to the same concentration as that in the surrounding water (source


The skin is one of the most important organs in fish. It has three basic components: the dermis (inner layer), the epidermis (outer layer), and the scales. The scales are embedded in the dermis, which is responsible for providing colour. Mucus is made by the epidermis and helps to protect the cells. It has anti-fungal and anti-bacterial properties and plays a role in immune function (Wainwright & Lauder 2017). Any type of skin lesion or scale loss can have serious consequences for fish, since healing in an aqueous environment can take a long time and wounds can get waterlogged. Just imagine, for example, trying to heal a paper cut on your finger by keeping it submerged in a glass of water for a week. The whole healing process would take much longer and you would be more exposed to bacterial infections. For all these reasons it is a good idea to use plastic gloves when handling live fish so as not to damage their skin.

The lateral line is part of the skin organ and consists of perforated scales with cilia (short microscopic hairs that can move) that are connected to the nervous system and provide information about water movement around the fish and pressure (constituting a sense organ not found in mammals). This allows fish to hunt at night or move in very opaque water by sensing the vibrations around them. The lateral line also has culinary importance, since cutting along this line in a cooked fish will separate the meaty upper section from the visceral section below.

Finally, as a curiosity, several recent studies have related skin colour to fish personality. For example, the colour of the dermis on the dorsal area of salmon (between the dorsal fin and the head) is darker or has more dark spots in fish that are more aggressive (Castanheira et al., 2017)


Fins can be used as indirect indicators of fish health and welfare. We want to avoid fraying of the fins (when the skin comes apart between the rays), fin erosion (white colouring at the tips of the fins), necrosis (dead cells on the fins), or discoloured spots, the latter of which may indicate the presence of parasites.

Dorsal fin

Normally fish have one dorsal fin, but they can also have two (one after another, as in sea bass). The dorsal fin is mostly used to help maintain the fish in an upright position. It is supported by rays which are often erectile to allow the fish to ‘open or close’ it depending on signalling requirements. Tilapia has a large dorsal fin with pointed rays that can easily cut innocent hands that want to grab it out of the water. The number of rays per fin can also be used to identify the species of fish. For example, rainbow trout have between 10-12 rays on their dorsal fin while brown trout (not normally grown in aquaponics) have around 13-14.

Adipose fin

This is a rather short and fat fin which is common in salmonids, but whose function is unclear. It is full of fat and appears to have sensory neurons. Sometimes it is cut off in farmed salmon to differentiate them from wild salmon but Reimchen & Temple (2004) found that fish without an adipose fin have a higher tail beat amplitude, indicating that it has a role in natural swimming behaviour, and that cutting it off probably has a negative effect on welfare.

Caudal fin

This is the largest and most powerful fin and is directly connected to the spine. It is used to thrust the fish forward. Like the tail of piglets, it can also be nibbled by other fish or get eroded by being rubbed on different surfaces. The tail is also important for measurement purposes (Figure 3). Apart from weighing the fish, aquaculturists often measure the standard length (from mouth to the beginning of the tail) and fork length (from mouth to the fork at the tip of the tail).

Anal fin

This fin is posterior (behind) the anus and urogenital pore on the ventral side of fish. Sometimes referred to as the cloacal fin, it is also important in stabilizing fish when swimming, so that they do not roll over onto their sides.

Pectoral and ventral fins

Close to the operculum fish have pectoral fins, which roughly correspond with the arms of terrestrial mammals, and below them are the ventral or pelvic fins, which roughly correspond with ‘legs’. In some fish, generally those considered to be ‘less evolved’ (i.e. those which have changed less over time compared to their ancestors), like salmonids, the ventral fins are further down the trunk region, while they are closer together in more modern fish (such as tilapia). The pectoral fins help fish to move up and down while the ventral fins are more important in stopping movement.


Figure 3: Example of fish length measurements for a tarpon fish. For standard weight equations, the total length is used, which includes the caudal fin (source

Copyright © Partners of the [email protected] Project. [email protected] is an Erasmus+ Strategic Partnership in Higher Education (2017-2020) led by the University of Greenwich, in collaboration with the Zurich University of Applied Sciences (Switzerland), the Technical University of Madrid (Spain), the University of Ljubljana and the Biotechnical Centre Naklo (Slovenia).

Please see the table of contents for more topics.

[email protected]

Stay up-to-date on the latest Aquaponic Tech


  • Our Team
  • Community
  • Press
  • Blog
  • Referral Program
  • Privacy Policy
  • Terms of Service

Copyright © 2019 Aquaponics AI. All rights reserved.