Fish Hatchery and Nursery Diseases: How to Protect Eggs and Fry

April is the busiest time of year in a Bangladeshi fish hatchery. A 2023 study of hatcheries in the south of the country found that the peak season for seed production runs from March to June, the months when grow-out farmers stock their ponds. It is also the season when a single outbreak in a hatching jar or a nursery pond can wipe out millions of eggs and fry within days.

Improved fish farming has spread fast in Bangladesh, and quality fry have become one of its most important inputs. Hatcheries began to spread across the country from the early 1990s, and disease in hatcheries and nurseries has since become a regular worry for hatchery owners and fry growers, because sick fry die quickly and healthy-looking fry can carry infection into the farmer's pond.

This guide, published in April 2025, explains why eggs and fry fall ill so easily, the main groups of disease found in hatcheries and nurseries, how each is prevented, which treatments the authorities describe, which old remedies are no longer advised, and where a hatchery owner can get help. Every dose given here is attributed to the authority that states it.

Hatchery seed is the starting point of Bangladesh's pond fish farming. A peer-reviewed study by Hazrat Ali, Ben Belton and colleagues, published in Frontiers in Aquaculture in July 2023, cites the Department of Fisheries (DoF) to show that fish seed production rose from 276 tonnes in 2002 to 671 tonnes in 2021. Over the same period aquaculture output grew from 786,604 tonnes to 2.64 million tonnes, and pond productivity rose from 2,580 kg per hectare to 5,129 kg per hectare.

The study surveyed 66 hatcheries in seven southern districts between May and August 2022: 42 carp and catfish hatcheries, 16 tilapia hatcheries and 8 crustacean hatcheries. It found that the number of hatcheries in those districts had grown by 15 per cent over a decade, with fish hatcheries up 27 per cent and crustacean hatcheries down 47 per cent. Most carp and catfish hatcheries bred their fish by pituitary gland injection (87 per cent), with synthetic hormone (11 per cent) and human chorionic gonadotropin (2 per cent) used by the rest.

Disease was a real but uneven problem. Eighteen per cent of the hatcheries reported diseases or water-quality problems, although the average loss from mortality was only 0.71 per cent of seed sales value. The authors also note earlier research describing disease as the most significant challenge in hatcheries, because seed can die abruptly. In the freshwater prawn sector the damage was far worse: prawn post-larvae production fell by 98 per cent between 2013 and 2021, which the study links to problems with an unidentified disease in prawn hatcheries.

Heat adds to the risk. In November 2023 the Bengali edition of The Daily Star reported from Jashore, which it said supplies 60 to 70 per cent of the country's demand for spawn (renu), that people in the trade said up to 80 per cent of spawn can be lost when temperatures stay at or near 40 degrees Celsius.

Fisheries scientists explain that, as in other animals, a fish's immune system plays the central part in resisting disease. It works constantly against the pathogens that are always present in pond and tank water, and keeps a healthy fish healthy.

Eggs, spawn and young fry in hatcheries and nurseries are naturally fragile. Their immune systems are not yet mature, so they fall ill far more easily than grown fish. Crowding in jars, tanks and nursery ponds lets an infection pass from one fish to the next very quickly.

The problem does not stay in the hatchery. Fry moved from an infected hatchery to grow-out ponds carry the pathogens with them, and the infection can then kill the fry stocked there. This is why the health of hatchery seed matters to every farmer who buys it, not just to the hatchery owner.

Stress is the usual trigger. Poor water quality, sudden swings in temperature, organic pollution from uneaten feed and dead material, and a high stocking density all weaken young fish and help bacteria and parasites take hold. The Food and Agriculture Organization of the United Nations (FAO), in its 2005 technical paper on the responsible use of antibiotics in aquaculture, says the need for medicines should be reduced through good husbandry, hygiene and vaccination, so that drugs are kept for treating disease rather than preventing it.

Fish hatcheries and nurseries commonly suffer from nine kinds of disease or infestation:

• fungal (water mould) diseases, mainly of eggs and spawn
• viral diseases
• bacterial diseases
• environmental diseases caused by poor water and handling
• parasitic diseases in general
• myxosporidiosis, caused by spore-forming myxozoan parasites such as Myxobolus
• louse infestation, caused by the fish louse Argulus
• trichodiniasis, caused by the ciliate Trichodina
• worm infections, such as gill flukes

Each group needs a different response. Some can be prevented almost entirely by good hygiene, some respond to treatment, and against viruses there is, in practice, only prevention. The sections below take them in turn.

Fungal infection, caused mainly by water moulds of the genus Saprolegnia, attacks fish eggs and spawn above all, and is a serious problem during hatching. Saprolegnia is often called cotton mould because it forms white or grey fibrous patches. It feeds on dead material and takes advantage of injured or weak tissue.

In a hatching jar the mould settles first on dead and unfertilised eggs. From there it spreads to the healthy eggs around them and, if nothing is done, can destroy the whole batch. The University of Florida's extension service (UF/IFAS) makes the same point: dead eggs should be removed promptly because they are a source of infection for the healthy eggs beside them.

Prevention is therefore mostly a matter of hatchery routine:

• wash the eggs and keep incubation equipment clean
• remove dead, damaged and unfertilised eggs as early and as often as possible
• increase the water flow through jars and incubators
• reduce the number of eggs held in each jar or tray

Where a treatment is needed, UF/IFAS, in its guide to formalin revised in December 2022, says formalin is approved by the U.S. Food and Drug Administration for controlling water mould on fish eggs, at 1,000 to 2,000 mg per litre for 15 minutes. It warns that formalin is not the preferred treatment for fungal or bacterial infections on fish themselves, that formaldehyde is a known carcinogen to be handled only with gloves and eye and breathing protection, and that strong aeration is needed whenever it is used. These are U.S. figures; a hatchery in Bangladesh should confirm the product and dose with its upazila fisheries officer.

Older Bengali hatchery guides, including the earlier version of this article, called malachite green the best and most reliable treatment for fungal disease and gave rates for using it on eggs and in ponds. That advice is out of date and has been removed here.

Malachite green is an industrial dye. Hong Kong's Centre for Food Safety, a government food regulator, explained in June 2019 that the Joint FAO/WHO Expert Committee on Food Additives (JECFA) has found there is no safe level of residues of malachite green or its metabolites in food that represents an acceptable risk to consumers, and that the dye may be both genotoxic and carcinogenic. It is prohibited for use in food-producing animals in many countries.

This matters for Bangladesh's fish trade as well as for consumers. Residues of banned drugs in exported shrimp led to rejections in European markets, and in January 2010 Bangladesh's parliament passed the Fish Feed and Animal Feed Act, which requires feed makers and traders to be licensed and restricts antibiotics, hormones and other harmful substances in fish and animal feed. Hatchery owners should rely on hygiene and on treatments approved by the fisheries authorities.

Viruses cause some of the most damaging losses among young fish. Grass carp haemorrhagic disease, caused by the grass carp reovirus (GCRV), kills grass carp fry and fingerlings. A study published in BMC Genomics in June 2017 describes it as one of the most serious diseases of grass carp. The virus belongs to the genus Aquareovirus, also infects black carp and some small wild fish, and one strain caused 80 per cent mortality in yearling fish.

Koi herpesvirus (KHV) causes a highly contagious disease of common carp and its ornamental form, the koi. Its signs include mottled and bleeding gills, sunken eyes, pale patches and changes in behaviour, and fish that survive it can remain carriers of the virus for life.

Fisheries scientists agree that there is essentially no treatment for viral diseases of fish. Regular cleaning and strict biosecurity are the only real defence. In practice that means buying broodfish and seed from known healthy sources, keeping new fish apart before they join the main stock, disinfecting nets, buckets and jars between batches, and keeping wild fish and dirty water out of hatchery tanks.

Bacteria are a common cause of death among fry in hatcheries and nurseries. The main culprits are motile Aeromonas bacteria and, in brackish water, Vibrio. They act either as primary pathogens or as opportunists that invade fish already weakened by stress. Tail rot and fin rot are usually caused by these bacteria.

For carp fry, haemorrhagic septicaemia caused by Aeromonas hydrophila is a serious problem. This bacterium lives in fresh and brackish water in warm climates and is widely regarded as a major fish pathogen; it rarely infects healthy fish but takes hold readily when their defences are down.

Deteriorating water quality, temperature swings, organic pollution and high stocking density all play a major part in bacterial infection of fry, including the swollen-belly condition farmers call dropsy. Correcting these causes, by changing water, cutting feed, removing dead fish and thinning the stock, comes before any medicine. The earlier version of this article gave a potassium permanganate rate for dropsy; no fisheries authority source for that rate could be found, so it has been left out.

Antibiotics need particular care. FAO's 2005 technical paper lists oxytetracycline among the antibiotics authorised for aquaculture, including for haemorrhagic septicaemia caused by Aeromonas hydrophila, and recommends that antibiotics be used only for treating disease, not for prevention. It also explains that every veterinary medicine needs a withdrawal period, the time after treatment before fish can be harvested for food, so that residues stay below safe limits. The dose, the duration and the withdrawal period should come from the upazila fisheries officer or a fish health specialist, not from guesswork.

Parasites are a constant problem in nursery ponds. Trichodina is a disc-shaped ciliate that lives on the gills, skin and fins of fish and multiplies by simple cell division, so its numbers can rise quickly on crowded fry. Myxozoan parasites such as Myxobolus form spores in fish tissue and cause myxosporidiosis.

The fish louse Argulus is a small crustacean that clings tightly to its host. Young lice feed on mucus and skin cells, and older ones feed on blood. Gill flukes of the genus Dactylogyrus, found mainly on the gills of carp and related fish, attach themselves with hooks and complete their life cycle on a single host.

Formalin is one of the standard treatments against external parasites. UF/IFAS says it is extremely effective against most protozoans and against some larger parasites such as monogenean flukes, but is not effective against internal infections. Its guide gives 12.5 to 25 mg per litre as a prolonged bath, the lower figure for sensitive or very sick fish, and up to 250 mg per litre as a short bath of 30 to 60 minutes in systems with high water flow.

The same guide discourages formalin in ponds. It is expensive in the volumes a pond needs, it removes dissolved oxygen from the water and it kills algae, which can lead to an oxygen crash and a fish kill. Fish that dart, gasp or try to jump out of the water during any chemical treatment should be moved at once into clean water.

Hatcheries in Bangladesh work under the Fish Hatchery Act, 2010 (Act No. 14 of 2010), which aims at the production of quality spawn, post-larvae and fry. According to the FAO legal database FAOLEX, no one may run a hatchery for commercial purposes without registration, and the Director-General of the Department of Fisheries or an authorised officer may visit any hatchery at any time and inspect its equipment, chemical products and breeding practices.

The Bangladesh Fisheries Research Institute (BFRI), founded in 1984 with its headquarters in Mymensingh, is the national body for fisheries research. Banglapedia notes that its Freshwater Station in Mymensingh runs a carp hatchery and experimental ponds, and that it has stations at Chandpur, Paikgacha in Khulna and Cox's Bazar.

A hatchery owner who sees eggs turning white and furry, fry gasping at the surface, red patches, swollen bellies or a sudden rise in deaths should take samples to the upazila fisheries officer of the Department of Fisheries without delay. The officer can arrange diagnosis and advise on approved treatments and doses, and on whether a batch should be destroyed rather than sold on to farmers.

Photo: syed sajidul islam / Wikimedia Commons (CC BY-SA 4.0)

Sources: The Agro News (Staff Correspondent), Frontiers in Aquaculture (Ali, Belton and others, July 2023), The Daily Star Bangla (November 2023), University of Florida IFAS Extension (Use of Formalin to Control Fish Parasites, revised December 2022), Food and Agriculture Organization of the United Nations (Responsible use of antibiotics in aquaculture, 2005), Centre for Food Safety Hong Kong (June 2019), BMC Genomics (June 2017), Food Safety News (January 2010), FAOLEX, Banglapedia, Wikipedia