Fish Management from Egg to Fry

Neonatal Management
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Similar to other species, the management of early stages of life are critical to future success of farmed fish.


In this section of the Neonatal Management FAAST Review we will focus on raising Salmonids (salmon, trout, and whitefish) and cover:

For more information on rainbow trout farming in Ontario and how to reduce antimicrobial use, and improve biosecurity, be sure to visit the Antimicrobial Stewardship in the Ontario Aquaculture Industry FAAST Review.


The National Farmed Animal Care Council has worked with researchers, producers, and other industry stakeholders to produce the first standard of care for the aquaculture industry: The Code of Practice for the Care and Handling of Farmed Salmonids. The Code of Practice is set to be released to the public in its final version in the fall of 2021. Information on the Code and its development, as well as opportunities to provide input or comment can be found here: 

Code of Practice for the Care and Handling of Farmed Salmonids

Broodstock Management

Egg production and quality of eggs is related to not only the genetics of broodstock but also their rearing conditions.


Feeding: Quantity and Quality

Feeding and nutritional quality of broodstock diets can have both direct and indirect effects on egg production, egg size, and egg quality. Specifically, feeding broodstock half or three-quarters of their recommended daily ration (0.5% of body weight per day) through the year can result in up to a 25% reduction in egg production8. Insufficient feeding can also lead to a lower proportion of fish spawning. Restriction of feed at the beginning of the development of the ovaries will also reduce egg production. For these reasons, it is recommended that producers feed 1% of body weight per day with grower pellets. This will lead to high egg production without a significant increase in the weight of broodfish11. Work with your nutritionist or feed supplier to ensure that you are feeding your broodstock a well-balanced diet with adequate amounts of protein, essential fatty acids and antioxidant nutrients to achieve the highest egg quality12.

Day Length Photoperiod

Manipulations of the photoperiod can be used to alter the rate of change of daylength to advance or delay maturation of the oocytes within the fish. Long days early in January to April, before longer day lengths (June), help to stimulate an earlier spawning. However, long days following the peak in day lengths in September to December, would produce a delay of spawning. In contrast, exposure to short days produce different responses. Short days in December to March, where they are early in the reproductive cycle, would produce a delay in egg maturation, whereas exposure to short days in the spring (April to June), produces an advance of spawning.

Photoperiod and temperature also interact in cueing the final maturation and spawning. In a 2010 study, the highest frequency of spawning and egg fertility and survival was found when broodstock were exposed to temperatures of 9-15°C during oocyte development and 12°C one month prior to ovulation13. Importantly, a significant reduction in fertility and survival will be seen at temperatures over 18-21°C.

A Note on Arctic Charr

While temperature tends to exert a minor influence on the reproductive cycle in most salmonids (when compared to photoperiod), this is not the case for Arctic Charr. Spawning in this species is inhibited when the water rises above 10°C, and the process of over-ripening (changes inside the egg that negatively affect egg fertilization) is greatly accelerated by temperatures above 5°C14.


Other Factors

Water quality parameters and stocking density also need to be closely monitored to have the highest success. While the ideal stocking density likely depends on a variety of farm factors, it is suggested that a stocking density should be over 10 kg/m3,8, but below 40 kg/m3,8 to improve reproductive success.

Receiving and Disinfecting Eggs


After stripping unfertilized eggs from the females, eggs are mixed with milt (or sperm) for a set time (e.g. around 60 seconds) where they are gently mixed together (very important not to have water in this stage). It is very important to ensure that the eggs and milt are handled carefully as rough mixing or handling will lead to milt losing their ability to fertilize eggs and eggs dying. It is also important to evaluate the motility of the sperm to ensure fertilization will be a success. When eggs are fertilized a small volume of fresh water should be added to promote hardening of the egg with fertilization. White, unfertile eggs should be removed at this time.



If receiving eyed eggs are being shipped to the farm, the first step upon receipt is tempering, or gradually bringing the eggs up to incubation temperature of your hatchery over a 30 minute to 1 hour time period.


This is done by:

  • Measuring the temperature of the eggs in the shipping container and adjusting the temperature of the container the eggs will be placed into to match the temperature of the eggs
  • Gently adding the eggs to the water, then adding small amounts of clean water from the hatchery to gradually raise the temperature of the eggs
  • It is recommended to gently stir the eggs in the tempering process to ensure adequate water circulation

In order to prevent introduction of disease organisms into your hatchery, it is recommended to complete the tempering process outside of the hatchery and discard all shipping containers.


Source: Centerpin Angling



Eggs are externally disinfected at green and/or eyed stage to prevent infection with bacteria, fungi, parasites and viruses. Disinfection is recommended for all batches of eggs prior to incubating, especially when using eggs from a wild or captive broodstock, another facility, or outside source. The process of disinfecting the eggs should be completed on arrival to the fish hatchery in a separate area to the incubation and rearing areas.


Iodophors have become the preferred egg disinfectant as they are the most reliable surface disinfectants that can be used to control the spread of fish pathogens with a wide margin of safety.

Iodophors (water-soluble product containing iodine) have been found to be effective to prevent the spread of bacteria (Aeromonas salmonicida, Flavobacterium columnare, Cytophaga psychrophila, Vibrio anguillarum, Yersinia ruckeri), viruses (infectious hematopoietic necrosis virus, infectious pancreatic necrosis virus, infectious salmon anemia virus, and viral hemorrhagic septicemia virus), and fungal/mycotic agents1. It is recommended to administer the iodine as a 10 minute bath at 100 ppm of free iodine2. It is important to note that if eggs are intended for human or animal consumption, iodine products should not be used.

Other Products

Other disinfectants include hydrogen peroxide and formalin. Hydrogen peroxide disinfectants have also been found to be effective against bacteria, viruses, and fungal/mycotic agents. Formalin may also be used but due to concerns about human safety, its use should be discouraged for use in egg disinfection as there are better alternatives.


To determine which product will work best on your farm, work with your veterinarian and other advisors to determine the specific products and dosages to use on your farm. 


Disinfection Conditions


During disinfection, it is also important to consider that the eggs are very sensitive to:

  • pH
    • Monitor the pH of the disinfectant solution
  • Oxygen
  • Water temperature
    • Water temperature should be the same as what the eggs will be incubated in
    • Should not change more than 3°C
  • Direct sunlight


Ensuring that the proper conditions are maintained during disinfection will prevent excessive egg loss.

Don’t Forget to Disinfect Your Tools & Equipment!

During the disinfection process, it is important that proper disinfection of hands, boots, all equipment, and working area is done. Specifically, change gloves, wash boots, and additional equipment between handling eggs prior to disinfection and when the eggs are clean. You might also consider having two people so that there is one person dedicated to handling the eggs before disinfection and placing the eggs in the disinfectant solution and another person that handles the clean eggs following disinfection.

Egg Incubation

All equipment used for handling eggs should be disinfected prior to use to minimize the chance of disease transmission between blocks of eggs. As a result, the incubator should be thoroughly disinfected before use if possible.

The period of incubation is critical in the prevention of fungal growth on eggs3. Critical principles to maintain throughout incubation to prevent the growth of the fungus and minimize egg loss are:


Adequate water flow and quality (including dissolved oxygen levels) 

  • Water quality
    • Clean water is critical, especially in this stage, as some sources of water (especially surface water) can contain parasites and other pathogens that could attack eggs and fry. In addition, some surface waters could contain suspended solids that could clog equipment or smother eggs and clog gills of fry
    • While most well water is free of fish pathogens and solids and doesn’t need filtration, it typically has low levels of oxygen, meaning the water will need to be aerated. Supplementing oxygen so that dissolved oxygen is near saturation (> 7 mg/L of dissolved oxygen) is critical as hypoxia reduces growth of embryos prior to hatch4
    • Ensuring that the water quality is adequate is absolutely critical to help reduce egg loss


  • Water flow
    • Ensuring water flow is high enough is also critical. During development, eggs can excrete harmful material that, when accumulated, can cause harm to the eggs. Maintaining a constant flow of water will allow for continuous removal of this material. Recommended water flow will vary depending on the type of incubator used, however, it is suggested to have water pass through the eggs at a rate of 11 to 18 L/min in upwelling incubators


Check out this report developed by University of Guelph researchers on the Development of Environmentally Responsible Techniques and Practices for Freshwater Aquaculture in Ontario, for the Ontario Sustainable Aquaculture Working Group. The report describes methods for measuring and monitoring water flow.


Optimal and consistent temperature

  • Incubation temperature is commonly used to manipulate hatch date in salmonids with lower incubation temperatures causing longer time to hatching and higher incubation temperatures causing shorter time to hatching. Optimal temperatures have been determined to be between 7-10°C to maximize survival, particularly for rainbow trout5. Having a consistent temperature will also improve survival


Keeping egg hatching baskets from being overcrowded

  • Suggested to have 0.2 m2 per 10,000 eggs6


Protect against direct sunlight

  • Eggs of some species are particularly vulnerable to ultraviolet light and rays of the visible spectrum. Therefore, diffused light or darkness in the hatchery is recommended


Dead eggs should be removed regularly to limit fungal infections

  • Removing dead eggs can be more effective than chemical treatment, however, is time consuming and labour intensive


Chemical treatment of water

  • Chemical treatment during incubation can help to control the fungus Saprolegnia, where a dilute formalin solution (dilution of 1:600) is added to inflowing water for 15 minutes daily up to 24 hours prior to hatching. As an alternative to formalin, which has human health risks, hydrogen peroxide can also be used to control fungal infections as well, where 500 ppm is applied for 15 minutes every other day


Source: Cedar Creek Farm

Larval Management

Maintain Oxygen-Rich Environments

The newly hatched larva has no mouth, gut, vent, gills, or air bladder. It relies on the yolk sac to provide material and energy for growth and development. As a consequence, fish larva requires an oxygen-rich environment, as oxygen exchange occurs through diffusion and not through the gills. Try to maintain dissolved oxygen close to saturation.


Consistency is Key

Similar to egg incubation, a suitable temperature is required for development, and rapid changes should be avoided during the larval stage as it may kill the larva. It is suggested to maintain the temperature between 7-12°C to maximize survival. Continuous exchange of water is also critical to remove waste materials produced by the larva.


Keep Them Clean

In addition, separation of freshly hatched larva from egg shells and spoiled eggs will also protect against exposure of the larva to bacteria and fungi that could develop. This can be done by providing ample exchange of fresh water and siphoning of dead and decaying larvae. During this period larvae are sensitive to chemicals including formalin; therefore, a clean rearing environment is the only option for prevention of fungal infections


Rearing Fry 

When fish begin to swim-up to the surface, the thin yolk sac has been absorbed. At this point, the fish are classified as fry (defined as the stage when fish have developed to a point where they are capable of feeding themselves and no longer rely on a yolk-sac for nutrition). This stage is particularly critical to develop productive and healthy fish. There are similar requirements for the fry nursery area including:


Excellent water quality

  • Free of toxic matter and organic pollution, for example low levels of3,8:
    • Ammonia: 0.012 mg/L
    • Nitrite: < 0.015 mg/L
    • Nitrate: < 3.0 mg/L
    • Hydrogen sulfide: < 1.0 ug/L

Prevent drastic changes in water temperature or oxygen levels!


Precise feeding

  • Unlike other stages, the fry require precise feeding to ensure their growth and survival as lack of suitable nutrition is one of the main causes of mortality
  • Fry should be fed at the latest when approximately 50% have reached the swim-up stage. At this stage of development, fry should be offered and consume over 10% of their body weight per day in feed for the first 2 to 3 weeks. Fry feed should have a particle size range of 0.3 to 0.6 mm with 45-50% crude protein and 12-14% fat and offered preferably on a continuous basis using an automatic feeder or hand feeding where feed is provided every 15 minutes if possible but not less than hourly. A sign of insufficient feeding is an increasing difference between individual sizes of developing fry and cannibalism in severe cases
  • Excess feed and fish waste should be removed from the troughs used to rear the fry daily
  • Work with your nutritionist or feed supplier to develop a feeding program for your farm


Watch for signs of disease

  • It is also necessary during fry production to evaluate a proportion of the fry each day to identify potential diseases that could be occurring in individuals before it spreads throughout the group.
  • Some diseases that could occur during this stage include:
    • Bacterial cold water disease, fungal vasculitis, and enteritis
      • Signs of acute disease include lethargy, protrusion of the eyeball(s), dark skin pigmentation, pale gills, loss of appetite, and a high level of mortality, whereas, a chronic form is characterized by erratic swimming behavior, blackened tails and spinal deformities in many of the fish9
  • Bacterial gill disease
      • Clinical signs of disease include loss of appetite, lethargy and little or no response to external stimuli. Fish will also lie listlessly on the side or top of the tank or trough and will breathe laboriously. Mortalities can be extremely high if not treated10
  • Work with your veterinarian to aid in the identification of signs of certain diseases and how to properly treat or prevent these diseases from occurring on your farm


Clean and disinfect fry troughs between groups

  • Between groups of fry, it is also important to clean and disinfect the fry troughs using products such as hypochlorite solution or an approved quaternary ammonium disinfectant to help control various disease causing pathogens



Take Home Messages

The rearing of the early stages of development of fish is critical to ensure health and productive fish of the future. Work with your veterinarian, nutritionist, and other advisors to tailor a program to your farm to help prevent and control disease while ensuring optimal productivity of your fish.


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  2. Hinshaw, J.M., and S.L. Thompson. 2000. Trout Production: Handling eggs and fry. SRAC Publication No. 220.
  3. Demeke, A., and A. Tassew. 2016. A review on water quality and its impact on Fish health. International Journal of Fauna and Biological Studies. 3:21-31.
  4. Wood, A.T., T.D. Clark, N.G. Elliot, P.B. Frappell, and S.J. Andrewartha. 2019. Physiological effects of dissolved oxygen are stage-specific in incubating Atlanic salmon. Journal of Comparative Physiology B. 189:109-120.
  5. Weber, G.M., K. Martin, J. Kretzer, H. Ma, and D. Dixon. 2016. Effects of incubation temperatures on embryonic and larval survival in rainbow trout. J Applied Aquaculture. 28.
  6. Hoitsy, G., A. Woynarovich
  7. FAO. Artificial propagation of finfish.
  8. Okumus, I. 2002. Rainbow trout broodstock management and seed production in Turkey: Present practices, constraints and the future. Turkish Journal of Fisheries and Aquatic Sciences. 2:41-56.
  9. Starliper, C.E. 2011. Bacterial coldwater disease of fishes caused by Flavobacterium psychrophilum. Journal of Advanced Research. 2:97-108.
  10. Speare, D.J., and H.W. Ferguson. 1989. Clinical and pathological features of common gill diseases of cultured salmonids in Ontario. Can Vet J. 30:882-887.
  11. Bromage, N., J. Jones, C. Randall, M. Thrush, B. Davies, J. Springate, J. Duston, and G. Barker. 1992. Broodstock management, fecundity, egg quality, and the timing of egg production in rainbow trout. Aquaculture. 100:141-166.
  12. Izquierdo, M.S., H. Fernández-Palacios, A.G.J. Tacon. 2001. Effect of broodstock nutrition on reproductive performance of fish. Aquaculture. 197:25-42.
  13. Pankhurst, N.W., and H.R. King. 2010. Temperature and salmonid reproduction: Implications for aquaculture. Journal of Fish Biology. 76:69-85.
  14. Gillet, C. 1993. Egg production in Arctic charr (Salvelinus alpinus L.) broodstock: effects of photoperiod on the timing of ovulation and egg quality. Canadian Journal of Zoology. 72: 334-338.