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In this section we will outline the most important internal organs of fish (Figure 4), underlining the main differences with mammals and some important facts that influence how fish should be maintained.


Figure 4: General internal fish anatomy (source


Fish have small brains compared to terrestrial vertebrates. For example, the human brain weighs approximately 1.4 kg and represents around 2% of the total body mass, but fish brains only represent 0.15% of their body mass. Nonetheless, unlike many vertebrates, fish brains are quite adaptive and maintain the ability to grow and change throughout life (they maintain the ability to produce new neurons; Zupanc 2009). Fish brains have three main regions: the forebrain (with the olfactory lobes and telencephalon), the mid-brain (optical lobes), and the hind-brain (cerebellum). Fish do not have a neocortex, which some scientists think is necessary to be fully conscious of pain, but other important structures exist that suggest they can feel pain, such as the amygdala, the cerebellum, and the pallium (outer layer of the telencephalon; for more information see Braithwaite 2010).


The heart is located just underneath the gills. Like the brain, it is quite small and relatively simple compared to terrestrial vertebrates, normally only weighing a few grams. It has a contractile ability to collect blood from the body and send it to the gills in a one-loop system which will be commented on more below under the section on respiration. It is a simple circuit with one atrium, one ventricle, and a conus which leads directly to the gills. There is no double circuit as in mammals, where the blood sent to the lungs returns to the heart to get pumped back to the body. In fish the gills ‘pump’ the blood to the body without sending it back to the heart.

Digestive system

The general makeup of the digestive system in fish is similar to other vertebrates, with a mouth, oesophagus, stomach, small intestine, large intestine, and anus. However, there is little demarcation between the different sections of the small intestine, nor is there an ilea-caecal valve separating the small from the large intestine. Carnivorous fish (like salmon) have a simple and short stomach and shorter intestines than herbivores (such as carp or tench), which may lack a stomach altogether and have a longer intestine with more pyloric caeca. The caeca are derivations of the digestive tract, which help to increase the total surface area for digestion and extract essential nutrients.

Abdominal fat

An important difference between wild and cultured fish is the amount of abdominal fat that accumulates in the latter. For example, sea bream from aquaculture will typically accumulate more visceral fat than wild sea bream, while fish that are fasted for longer periods have less fat than fish fasted for less time (Mozanzadeh et al. 2017).


The spleen is normally a dark red circular organ attached to the intestine. It helps to clean the blood, contains white blood cells, and is an important part of the immune system.

Liver and gall bladder

The liver is quite large and reddish, and beginners sometimes confuse it with the heart. It plays a vital role in detoxifying any organic or inorganic contaminants found in the food or water, as well as participating in protein synthesis, and fat and glycogen storage. Underneath the liver is the yellowish green gallbladder. Most fish do not have a distinguishable pancreas but rather Brockmann bodies, a collection of endocrine cells found along the digestive tract which can produce insulin.

Swim bladder

This organ is unique to fish. It can be filled or emptied to control buoyancy, and thus affects the amount of energy needed to swim. It can also be used to produce or receive sounds. Fish can be either physostomous (like trout), who can fill up their swim bladder via a pneumatic duct which is connected to the gut, or physoclistous (like bass), with no direct connection between the oesophagus and the entry to the swim bladder, so it must be filled up using a gas gland. Physostomous fish are better prepared for sudden changes in water height while it will take longer for physoclistous species. For all fish it is important to fill the swim bladder with air at an early stage of development, in order to assure proper growth and avoid spinal deformities (Davidson et al. 2011).


The kidneys are paired organs that are quite long and narrow, and dorsal to the swim bladder. They play an important role in blood homeostasis (i.e., maintaining appropriate levels of dissolved ions), which explains their substantial size. As in mammals, they are needed to ‘clean’ the blood, which is especially important in an aqueous medium where the concentration of different ions must be monitored continuously. It should be noted here that fish from fresh- and saltwater have adopted opposing methods to maintain appropriate levels of blood electrolytes. Freshwater fish have a higher concentration or ions in their blood than the surrounding water. Therefore, due to osmosis, the gills and kidneys of those fish must work to avoid absorbing too much water (H2O) and losing too many ions (they drink little and ‘urinate’ a lot). In saltwater the opposite occurs: fish drink/ingest more water and urinate little since the concentration of ions in their blood is lower than the surrounding water. In aquaponic units, care should be taken to ensure that the nutrient solution for plants is not having a negative effect on the fish due to inappropriate ion levels. At the end of the kidney there is a bladder to store urine, but it is very small compared to mammals, mostly because little urine is produced in comparison (as mentioned above, much of the nitrogenous waste is excreted by the gills).

Testes and ovaries

Most of the fish used in aquaponics will be used as food and will not mature sexually (breeders are kept in a separate installation). However, it is useful to know that sexual reproductive organs in fish are internal and start to develop deep inside the dorsal region of the fish near the head kidney. As fish mature, the gonads grow in size drastically towards the urogenital pore near the anus. During breeding season semen or eggs will be expelled for external fertilization.

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.

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