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Harvesting fish is one of the most important aspects of a high-quality aquaculture distribution chain. Whether you're eating fish from a home aquaponics system or a large commercial aquaculture system, knowing these methods will be very helpful.

Your harvesting method could also influence the quality of fish, therefore, good practices must be strictly observed in harvesting aquaculture products to maintain their marketability and secure safety for human consumption. Although different methods of harvesting are practiced in different regions of the world, there are still common practices that the aquaculture sectors are doing and some of those are listed below:

  1. Feeding must be stopped at least 24 hrs before the scheduled harvest to give fish enough time to empty their stomach especially if marketed in live condition, this practice could avoid polluting the water during transport.
  2. Harvesting must be done very quickly and early in the morning (just after sunrise) or late afternoon when the temperature is cooler to reduce the exposure of fish to the ambient temperature, reduce stress and to avoid mass mortality.
  3. If the harvested fish are to be sold dead, the fish must be washed with clean fresh/sea water after harvesting to remove any bacteria or weed and mud then, quickly stun the fish and chill them as soon as possible with the use of ice in clean washable containers.
  4. On the other hand, if fish are to be sold alive, a proper aeration system must be used and make sure not to overcrowd the tank. The water in the transport tank must have the same temperature, dissolved oxygen and pH levels with that of the water environment of the harvested fish. Before and even during transport, observe the fish and remove the dead ones if there is any.
  5. Always handle the fish with care and do not overfill the boxes with fish to minimize physical damage.
  6. Weigh the harvest and proceed to transport as quickly as possible. For traceability purposes, record of harvest must be maintained.
  7. Before and after harvest, all equipment must be properly cleaned, disinfected and kept in clean storage room. Contamination from any forms of chemical and microbiological hazards must be avoided all throughout the process.

Harvested Fish

Harvesting methods could differ among regions and it also depends on the kind of fish species to be harvested. The following summarizes the harvesting methods being used in certain countries practicing aquaculture.

Harvesting Fish from Aquaculture and Aquaponic Systems in the Philippines

In the Philippines, frequency of harvesting depends on the demand from the market. Especially in the case for milkfish and tilapia, fish farmers could either do total, partial or selective harvest. If the market price is high like during full moon wherein there’s little catch from the sea, the farmers will also take the chance to harvest the fish to maximize profit. Moreover, in times when farmers were facing financial struggle, they sometimes opt to do selective or partial harvest just to meet their needs. Harvest is done when the target size of the fish has been attained, usually 500g for milkfish.

Milkfish is known as the national fish of the Philippines. In harvesting milkfish, several methods could be used such as (1) total drainage, (2) pasubang, (3) seining and (4) electric shock method. Total drainage method is now seldom used as it gives a low-quality fish harvest since the harvested fish smells and tastes muddy.

The current method used is called “pasubang” which takes advantage of the swimming behavior of the fish which swim against the current. This method could be used for both total or partial harvesting. The method is very efficient and harvested fish are more clean (less muddy) than using the total drainage method. During harvest time, at low tide, the water in the rearing pond is partially drained and at high tide, brackish water can enter the rearing pond to make the fish swim through the gate towards the catching pond. When about 95% of the fish have been impounded in the catching pond, the pond gate will be closed. Then, the fish will either be seined, scooped or both depending on the size of the catching pond. Then, the rearing pond will be totally drained to catch the remaining fish. The harvested fish were then put into clean iced water and let them die with the least struggle thus preventing scale damage and preserving good flesh quality. On the contrary, seining is used when fish farmers would like to do partial harvesting. To kill the harvested fish, 2 blocks of crushed ice for every ton of fish is placed in a chilling tank or box and fish were then sorted per sizes. Metal tubs are usually used to transport the harvested fish to the market and crushed ice in a ratio of 1:1 is scattered on the fish in the metal tub. Amount of ice to be used is also adjusted according to the length of time needed for transportation until it reaches the market.

Another method used to harvest milkfish is the electric shock method. The same case with the pasubang method, fish were directed to swim towards the catching pond and once ready, the water level is lowered and to kill the fish, electrical shock will be administered in the form of induction coil. Fish will then be collected using a net and through this method, fish harvest are cleaner.

Harvesting Fish from Aquaculture and Aquaponic Systems in Europe

In Europe, harvesting process of cultured fish covers the period of fasting, collection and movement of the fish to slaughter and then stunning and killing. Due to the differences in physiology of various farmed fish species, it is not possible to identify a single harvest method that could be used for all. Farmed fish in Europe includes European eel, African catfish, rainbow trout, Atlantic salmon, Coho, Chinook salmon, European sea bass, gilt head bream, tilapia, Pangasius, Halibut, European turbot, Atlantic bluefin tuna and common carp.


Before fish collection, farmed fish needs to undergo fasting for a period of time depending on the water temperature and fish species but it could be from 1-5 days. For trout, their gut could be emptied within 24 h and, 3 days of fasting could depress their immune system. Moreover for salmon, 72 h of fasting is recommended. During this process, an empty gut causes a decrease in fish metabolic activity thereby reducing the building up of ammonia and carbon dioxide during crowding and transport. Furthermore, fecal contamination which can negatively affect the shelf life of the fish is prevented during processing.

Fish collection, transport and slaughter

In fish harvesting proper, the first thing to do is the crowding process. Fish held in nets are crowded by slowly lifting the part of the net or by inserting another net into the water. On the other hand, seine nets are used to facilitate crowding of fish grown in ponds, raceways, and tanks. It must be noted as well that different species of fish respond differently to crowding methods, however, process must be done slowly and with great care to avoid stress, injury and fish mortality. For Atlantic cod, before crowding, the cage depth needs to be reduced slowly in order to avoid swim bladder inflation. For salmon, crowding must be done progressively to ensure that the water remains deep to observe any signs of abnormality, asphyxia or even fish leaping out of the water.

After crowding, fish are then moved by brailing or pumping. Brailing is usually used for sea bream, sea bass and pangasius while pumping is widely used for farmed salmon. In brailing, to gather the fish from the water, large hand net or crane-operated nets are used. Brailing process could be classified as dry or wet. By tradition, dry brails are frequently used for convenience although bruising, crushing, injuries and abrasions could happen from contact with other fish, contact with the net and other hard surfaces. However, in wet brails, these could be avoided because water is collected and lifted together with the fish. For pumping, it is done by just putting a large bore tube into the crowded fish then, the pump will suck up the water and fish through the tube with the use of centrifugal or vacuum-pumping mechanism with transit time between 2 to 4 minutes.


Harvesting method also differs based on the scale of operation. In commercial scale production, automation may be required for efficiency and rapid fish harvesting. On the other hand, manual method of harvesting is done for smaller operations. Moreover, aside from maintaining a high-quality harvest, attention must also be given to bird predation and netting stress during the whole harvest procedure.

In harvesting sea bream, fish needs to be starved for such time (48-72 hrs.) based on the temperature and feeding rate. At 25 °C, 24 hrs. of starvation is enough already while at lower temperature, longer time of starvation would be necessary. During this period, the time could also be spent to clean the bottom of the tanks to ensure a clean fish harvest as well as to remove dead fish. During harvest time, a small trawl is used to persuade the fish to move towards the water inlet and through pumping or using dip nets, fish will be collected. Then, fish will be killed using thermal shock. Fish are placed into a stainless-steel tub with iced water saturated with CO2 to minimize fish stress. Then to proceed with packing for transport and delivery to the market, fish will be taken out of the iced water quickly to prevent loss of scale and preserving the appearance and freshness of the fish. It must be noted that fish must only be iced at most for 4-5 days before reaching the market.

In the case of sea bass, fish starvation depends on the water temperature. The technique of harvesting is the same with that of sea bream wherein dip nets or vacuum pumps are being used. Also, harvested fish were killed through asphyxiation in chilled water with slurry ice. The killing method must make the fish unconscious at the fastest time possible to ensure high product quality. There are also other procedures that could be done to kill the fish like spiking of the brain, blow to the head and destruction of the spinal cord. However, these methods are impractical to be used in commercial fish production and would need qualified personnel to do the procedure and that would entail additional cost. Moreover, most farmed fish are killed directly without prior stunning. Nevertheless, if required, common stunning procedure practiced in aquaculture production includes the following.

Electrical stunning

Used for rainbow trout, carp and other fishes exposed to electrical field. Electricity is used to stun the fish but may not necessarily kill them, so stunning must be followed by an effective killing method such as decapitation or percussion to lessen the stress that might affect fish quality of the final harvest. Variation in sizes, weight and fish location with respect to the stunning device when current is discharged however could influence the effectivity of this method. Plate electrodes could be used as a source of electricity.

Live chilling with CO2

This method is usually applied in salmon wherein fish are exposed to water having a temperature between 0.5 - 3°C and CO2 is added at low to moderate levels and saturated O2. This procedure however is unlikely to result in loss of consciousness in fish.

Asphyxia in air

From harvesting pond or tanks, fish are placed in free-draining boxes. However, this procedure is stressful for the fish and could negatively affect their flesh quality.

Harvesting Fish from Aquaculture and Aquaponic Systems in Japan

Some economically important aquaculture fish species in Japan are Japanese amberjack, red seabream, Atlantic bluefin tuna, ayu and eels. Eels are high commodity fish in Japan. Depending on the target market, they could be harvested when they reach 150 g to several kilograms. Before harvesting, feeding is stopped for 1-2 days. Then, the pond is drained and harvesting is carried out by seining or scooping the eels and size sorting is done rapidly using grading system and into the holding tanks to purge for a couple of days before delivery to the market and restaurants. To transport the fish, they are chilled and packed into a sturdy plastic bag containing enough water to just to ensure moist in their skin. The plastic bags are then filled with oxygen and transported to the market.

In addition, sea bream, parrot fish and Japanese flounder are in high demand and they are transported alive to restaurants and markets using live-hauling tanks in trucks. Comparing the market price of the fish caught in a conventional way and those hauled alive, the latter is more expensive to about 30-60% higher. Japanese always put priority on fish quality, freshness and safety of food products, thus they practice appropriate labelling of all fish and fishery products.

Technology advancement in Japan is so efficient even in the aquaculture sector and recently, artificial intelligence (AI) and Internet of things technology (IoT) has been developed by Nissui in collaboration with NEC to automate farmed fish measuring system in order to lessen the risk of stress from people handling the fish. The technology is able to measure the size of the fish and record the information by simply uploading the images of the fish as they swim around their tanks.

Tuna Industry in Japan specifically marketed by Kaneko Sangyo Co., Ltd. undergoes a strict processing method. The transported tuna from the farming sites were continuously subjected to strict temperature control and processed the tuna fillet with individual packaging with special film. In 2019, the company was able to develop successfully a Long Life Chilled (LLC) fresh tuna wherein under refrigerated storage, the shelf life of tuna could be extended up to 7 days after processing.

Harvesting Fish from Aquaculture Systems in the United States

Important aquaculture fish species in US includes channel catfish, trout, salmon, tilapia and hybrid striped bass. Harvesting of hybrid striped bass fish in the US is commonly done by pond draining and fish are collected in the catch basin with nets. The soft mesh knotless seine net that is usually used is 4 cm or larger. Generally, the size of fish to be harvested depends on the market demand. And, partial harvesting is practiced using larger mesh size net to make the harvest more size selective and gives the smaller fish time to grow more for the 2nd round of harvest.

Another harvesting method that has been practiced in the US is the fish elevator system. It is mechanically operated “Archimedes Screw” within a PVC pipe or fiberglass. Fish are harvested by lifting them from the pond and off loaded on a truck or tank system. Fish are then sorted by size using the built-it grader distribution in the system. The use of this system helps maintain the quality of the produced fish by minimizing scale loss, wounds and abrasions.

At the harvest site, in preparation for transport, fish could be packed on ice in boxes and loaded onto a refrigerated truck. Factors to consider in determining the amount of ice needed for transport includes, initial temperature of fish, time that fish needs to be on ice and the insulation efficacy of the transport unit. Fish flesh temperature should be maintained as close to 0°C as possible. In general, with good fish-ice contact, a 1:1 ratio of ice to fish weight is recommended to keep the fish in ice for about 12 hrs. Moreover, in fish processing, fish should be bled, washed and eviscerated as soon as possible. Hybrid striped bass in the US are marketed primarily in either live or whole fish on ice. Also, individual quick freezing (IQF) flash-frozen is also been practiced as secondary method. 

Clean and Healthy Fish

Best quality, healthy and clean fish is a priority in aquaculture sector. Even during harvest, contamination could possibly happen which may come from water, ice, workers hands, harvest equipment and unclean containers. This could be prevented if workers will wear appropriate personal protective equipment, use of ice made of clean fresh water and using containers made of non-absorbent material which are easy to clean to provide fewer microorganisms to thrive. Moreover, nets, equipment and containers used for harvesting must be wash with clean water and air dry before and after using them. More importantly, fish must be kept at cool temperature to preserve the quality and safety of the flesh and to slow down the possible growth of microorganisms.

Rena Santizo-Taan

PhD in Fisheries Nutrition

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