Manual for Bosanska Krupa Nov. 2009

                                                                                       By Linda Bollerup

  • A brief manual for the most common challenges in a recirculation system 


In this brief manual there will be an introduction to some common challenges for a recirculation system, hereunder daily routines, water chemistry, water quality and what to do if the values are too high, a few of the most common fish diseases and how to treat these and electrofishing. There will be focus on prophylactic action.


Fish in a recirculation system can’t escape which means that they have to stay in the environment no matter what happens and how bad the water quality is. It is always important to remember; that what you think is small deviations from normal can be fatal for fish.

A lot of different kind of fish diseases can be found in the wild fish in the river, but it might not be fatal for the wild fish, as it will be for the fish in capture. The reason for that is that the wild fish isn’t stressed and is better to handle diseases, also important is that the disease pressure is very low for the wild fish compared to the fish in the tank. The fish in the tank will experience a tremendous higher disease pressure than the wild fish and even a well conditioned fish in a tank can be sick and die.

The idea with a recirculation system is that the water should be used several times before it is flushed out of the system as waste water. This re-use of the water demands an overall good water quality and of course an observation of the water quality, so it is possible to react if the values vary. A recirculation system also demands an alarm system, so that you know if there is something wrong also if you aren’t at the hatchery. And of course there has to be a person who’s in charge and can react if there is an alarm. A recirculation system is very sensible and a small problem can develop and become a huge problem if there is no one to act on it.

There are also a lot of benefits in having a recirculation system, of course: It is possible at some level to control the water temperature, the flow, the water quality, diseases etc. and it is very good for the environment that the water is re-used several times. The future is to build recirculation systems and not flow through systems and to take the used water through a wetland before it goes back to the river again.


It can be hard to say if the fish fells okay and is in a good condition, but with some practice, learning lessons and an open mind it is possible to improve all the time.

With time you will learn how to handle fish diseases, bad water quality, a broken pump and other unpredictable problems. But of course: It is always better to prevent than to cure.


Figure 1: Eggs and newly hatched yolk sac fry,
The hatchery
The official opening Dec 2008.

Daily routines (and other routines)

There are some daily routines that are very important to do every single day, and there are some other routines that are important to make several times a week or if the fish are sick.


The reason why this is important is, by keeping a high standard of hygiene and cleanliness, you contribute to lower the risk that the fish become sick and you make sure that the biofilters are working. 


Every day you have to:

  • Go around and look into every fish tank, every tray and every filter system. Make a daily route which you can follow when you arrive at the hatchery in the morning and when you leave later in the day. In this way you can make sure, that fish are okay and you can react if there is something wrong. With some practice you can walk the tour fast and don’t spend a lot of time on it if you don’t want to. You can have a glance at the fish, biofilters and so on and most of the times quite easily see if there is something wrong.
  • Take away dead eggs and fish. It is very important to remove dead eggs and fish, otherwise they can infect the healthy eggs and fish and they can become sick. The disease pressure is a lot higher if there are dead organic material into the water close to the eggs and fish. It is also important for the water quality to remove the dead eggs and fish. By removing the dead eggs and fish you contribute to prevent diseases and bad water quality.
  • Remove organic waste material which means surplus feed and faeces. Dead organic material use a lot of oxygen when it is decomposed and it is also preferred place for bacterium.
    You can remove the dead organic material by flushing the tank and the trays. It is easily done and just remembers two very important things: Don’t flush too much water out at one time, make sure that the eggs or the fish have enough water, and make it carefully so you stress the eggs and the fish as little as possible.   
  • Check the water flow every day and adjust if it is necessary. The fish will get stressed if they have to struggle to stay at the same place in the water and they get easier sick and they are not able to exploit the feed. A guideline says that the flow is optimal if it is the length of the fish every two second.
  • Flush out from below the biofilters. This will remove the most polluted water from the system.


Several times a week you have to:

  • Measure the water quality, hereunder ammonia/ammonium, nitrite, nitrate, pH, oxygen level and temperature (see the next chapter for information about water treatment). If you measure the just mentioned parameters several times a week you can follow the development and pulsations and you can react. It might also be possible to see when it is time to return flush a biofilter. If you only measure once a week or even rarer, you can’t know what happened with the water quality in between the two measurements, and if you had measured it might have explained the stressed fish or maybe the dead fish. So with a recirculation system it is VERY IMPORTANT TO MEASURE THE WATER QUALITY.




It is a good idea to write down the energy consumption (water, electricity, heat) every day. In this way you can see if there is a leek in the water pipe line, a pump that really should not be turned on or other inadvertent consumption. In this way you can easily save some money.

It is also a good idea to have log book so you can write down the days work. In this way you can remember much more the next year when you have to do things again, and if you work on shift you then give your colleague an opportunity to know/read what happened on you shift or during the weekend. It is a cheap and good working tool.

Some times it is necessary to move the fish, to measure the length of the fish or other kind of things where you have to handle the fish. In such a time it is very important to do it as gently and carefully as possible. Always remember to stress the fish as little as possible. And if you have the ability to wait until the fish is in a better condition to be handled then you should do so.

In periods with start of a new system, for example if you have emptied the fingerling system and cleaned and disinfected the system, then you have to measure the water quality several times a day when you start to bring fish into the system again. The biofilters have been out of function and they have to be started up again from almost zero.

If you have some pumps that you don’t use every day, then start them up often to make sure that they in fact will work when you suddenly have to use them.

Always have several submersible pumps because you for sure need them some timeJ

Like any other domestic animal, fish do best if kept under hygienic conditions.

After a season’s use tanks and screens should be scrubbed out with a disinfectant solution and left dry for a while. Buckets, transportation tanks and any other equipment which comes in contact with the fish should be disinfected after use.

Hatchery equipment should be disinfected and stored dry when not in use.

Water quality

In a recirculation system the water can stay in the system for a long time and because of that it needs to be rinsed. The fish discharge waste to the water in the form of faeces and ammonia/ammonium (NH3/NH4+ ). The faeces are organic material that needs to be converted by bacteria in the biological filter. The ammonia is an end product of amino acids degradation and it is toxic for fish and it needs to be converted also in the biofilter, but by an other process than the faeces.


In the biological filter the following process is going on:


NH3/ NH4→ NO2- → NO3- → N2  (Nitrification and Denitrification))


Ammonia/Ammonium → Nitrite → Nitrate → Free Nitrogen (gas)


It is especially the ammonia and the nitrite that are toxic to fish and you need to measure these two parameters often and keep track of the amount of those two.


In water there is equilibrium between NH3 and NH4+ and the amount of NH3 and NH4+ depends on especially the water temperature and the pH (whether the water is acidic or alkaline with the pH scale being 1 – 14 where 7 is neutral and 1 acidic).  


Equilibrium into the water: NH3 + H+ ↔ NH4+  


Whether there is most of NH3 or NH4depends on the pH of the water. The lower the pH (acidic) the less in NH3 form, which is the most toxic.



Tabel 1. Indicative values for different parameters.




Normal range

Unfavourable level









0 – 2,5





0 – 0,5





100 - 200





70 - 100

‹40 and  ›250




10 - 20





6,5 – 7,5

‹6,2 and ›8,0

Figure 2. The influence from pH and temp. on the equilibrium of ammonia and ammonium

Most of the instruments that measure the amount of NH3 measure the amount of both  NH3 and NH4together. It is the NH3 that is interesting/toxic and you can find a good help in looking at a graph showing the distribution between NH3 and NH4depending on the pH and the temperature of the water (see figure 2).

There can be several reasons why you can encounter high level of ammonia and nitrite and there are also different things you can do if you experience high levels. Below there will be mentioned some of the most common reasons to too high level of ammonia and nitrite and what

to do if the levels are too high.

 Reasons to high levels of ammonia:

  • Too much feed which means too much organic material to the biological filter
  • Too fast increasing in feeding
  • Starting up a new system (or a system that have been disinfected)
  • Moving too many fish into a system too fast so the biological filter can’t keep up.
  • Medical treatment of the fish for example by using formalin
  • Large and fast pH fluctuations



What to do if there is too high levels of ammonia:

  • Lower pH by adding hydrochloric acid (HCL) carefully!
  • Temporary stop the feeding (be careful with the small fish)
  • Lower the temperature (not too fast)
  • Exchange some water (dilution effect)





Reasons to high levels of nitrite:

  • Starting up a new system (or a system that have been disinfected)
  • Large and fast pH fluctuations
  • Stressful factors such as medical treatment of the fish etc.


What to do if there is too high levels of nitrite:

  • Add salt (NaCl) in limited quantities
  • Temporary stop the feeding (be careful with the small fish)
  • Make sure that the oxygen content is high enough




Nitrate isn’t especially toxic to fish.  Anyway very high levels can be harmful, so it is a good idea also to measure the level of nitrate. The level of nitrate can also be used as an indicator for when it’s time for return flush the biological filter.


NO3- → N2  (Denitrification)


The denitrification is an anaerobe (oxygen free) process, which means that the bacteria need an oxygen free “pocket” to perform the chemical reaction.



The fish and the biofilters act best at the pH range 6 -8 (see table 1). The pH shouldn’t vary too much over a short time.



Most biological processes are depending on the temperature and many of these are faster with raising temperature. The converting of ammonia onto nitrite/nitrate is an example of that, but it has a limit at higher temp. The process is very slow at temperatures below 10 C, which should be kept in mind when starting up an empty system.


The salmonids have their temperature optimum meaning that there is a temperature they prefer for the best growth, utilisation of food, having the best immune system etc. They prefer a temp. around  16 C.


However, they can live in colder or warmer water, but crucial that the temp. doesn’t fluctuate too fast and that they aren’t transferred into water which isn’t more than 3-4 degrees different from what they came from. 

It is very important to know that oxygen is easier dissolved in cold water than in warm water so when the temperature of the water is raised you need to add more oxygen to the water or to exchange more water.


Oxygen: The fish uses more oxygen when the water gets warmer, when it has greater activity and when it is fed more. The fish can acclimate to a lower level of oxygen but they will get stressed and also the NH3 and NO2 that are present will be more toxic.


Common fish diseases

When fish become sick they change their behaviour and often they won’t eat. You often see that they start to swim around atypical and you might have to slow down the circulation in the tank because they weaken. Typically, for a start, it is just some of the fish that changes their behaviour and when you walk your daily tour in the hatchery, you have the chance to find out at an early stage in the disease and you might prevent a big disease outbreak.

In the text below, there will be a short description of some of the most common salmon fish diseases and how they might be treated. It is however important to remember that this text is not definitely and that a veterinarian should be consulted, when you have to use veterinary prescribed medication.

Disease may be caused by several things for example viruses, bacteria, fungus, parasites or it can be a nutritional condition or environmental condition.


Saprolegnia (fungus):

Saprolegnia is a fungus species. Fungal disease is frequently-occurring in salmon fish under artificial conditions where they swim lot closer together than in the wild nature and where they also get easily stressed. Fungal disease also occurs in the wild fish but mostly in the period of reproduction when they are hormonal stressed and they are fighting against each other.

Fungal disease is also often seen in eggs and in newly hatched fry.

 Fungus grows very well on dead eggs and fry (dead organic material), so it is of great importance to remove all the dead eggs and fry from the water every day. Otherwise it will spread out hyphae and spores and over growth healthy eggs and fry.  



Figure 3. Brown trout with saprolegnia.


Symptoms: Infected eggs look like cotton balls with characteristic white plaques (figure 3). A lot of infected eggs cluster together with apparently healthy eggs.

Bigger fish get well-defined white round spots; sometimes the spots are horseshoe-shaped.



  • The saprolegnia spreads very fast so it is important to remove dead material every day.
    If it is some bigger fish that are infected it can be a good idea to kill these so they wont infect the healthy fish.
  • Treatment with chloramin T: 15-20 minutes in the concentration as recommended on the label. Remember to stop feeding about 1 hour before treatment and until 1 hour after! The treatment is repeated for 3 days.
  • Treatment with formalin: 15 – 20 minutes in 0,01 % concentration (or as recommended on the label) in well oxygenated water. If you don’t have the ability to oxygenate then it is possible to bring down the height of the water before you put in formalin and then raise the height of the water in 15 min and afterwards take out the water from the tank in the same time you take in new water. Be careful with the treatment and supervise under the treatment and start up treating he fish in one tank and see how the fish behave.  The fish are normally treated three days in a row.
  • Salt (NaCl):  Be careful in using salt for eggs and fry. Normally they don’t tolerate as much salt as the bigger fish. Try to give them a small dose and then see how they react (only 2-3 ppt), before you give salt to all of them. Adult fish can easily be given a salt concentration at 9 -10 ppt (g salt/l water).



Furunculosis (Aeromonas salmonicida):

Furunculosis is a disease that results from the bacterium Aeromonas salmonicida. It is the most common bacterial disease in farmed salmonids.

Outbreaks are likely when the water temperature is 15 – 18 C or higher. The disease spreads by direct contact between the fish in tanks or through the water. Fish can retain low concentrations of bacteria in their tissue and become carriers without showing clinical symptoms.  




The disease develops after an incubation period of three to four days and young fish may die in large numbers without showing any symptoms than a slight loss of appetite and a little atypical swimming. Subacute infections can cause inflammation of the intestine and reddening of the fins and the gat. You often see a small slight increase in the number of dead fish, before the disease breaks out with full power.

Large fish or brood stock may develop the typical symptoms of the disease: Swellings or “furuncles” which can occur anywhere on the fish’s body. The swellings, which contain reddish pus, may burst either before or after death, releasing a mass of bacteria to the water and spreading infection.




  • Tribrissen (veterinary prescribed medication): 75 g/ ton fish in 8 days. Be careful with overdosing because tribrissen can also be toxic to fish, so if they start to swim odd (especially the big fish in the tank) then they might have been poisoned.
  • Oxolonsyre (veterinary prescribed medication): 13 g/ton fish in 7 days.
  • Ammoxocilin (veterinary prescribed medication): 200 g/ton fish in 10 days.
  • Florfenicol (veterinary prescribed medication): 10 mg medicine/kg bodyweight/day in 10 days.
  • Serious outbreak of furunculosis is best avoided by good husbandry, avoiding stressing the fish and by careful handling at all stages of growth.



Myxo bacterial disease:

The cause of this disease is an infection of the gill filaments by a myxobacterium. It is accompanied by mucus clogging the gills which may be the result of irritation from finely divided solids in the water or from dust from the starting feed.


Symptoms: The cause of this freshwater disease in salmon fry and parr is an infection of the gill filaments by a myxobacterium. It is usually accompanied by mucus clogging the gills which may be the result of irritation from finely divided solids.



  • Avoid over-crowding.
  • Filter the water to remove irritant debris.
  • Chloramin T: Treatment with chloramin T: 15-20 minutes in the concentration as recommended on the label. Remember to stop feeding about 1 hour before treatment and until 1 hour after! The treatment is repeated for 3 days.  


Fish and other aquatic organisms (invertebrates, amphibians, reptiles, birds and mammals) are affected by electric current when the electric tension of the body from tail to head exceeds a certain level. Under the effect of AC the fish are not attracted to some of the electrodes. At DC the electrodes have permanently either cathode or anode and the fish is attracted to the anode and repelled from the cathode.


Figure 4. Electrofishing in a small stream.


When the fish is in the electric field, it reacts on the difference in the tension arising between the head and the tail (body tension).

How the fish react on the DC depends principally of the species, the power of the electricity, the water conductivity and the temperature, but primary of the size of the fish, because voltage drop increases proportionally with the length of the fish.

The fish will react on the electric current in the water and start to move towards the anode (the positive electrode). The reason for that is that the muscle and nerve cells of all animals are based on very weak electric pulses, which maintain a constant difference between the inside and outside of the cell. It is these differences in potentials that are affected by electrofishing.

The electrofishing demands a well defined anode (positive electrode) which means that the electrofishing have to be done by the use of DC or unidirectional AC. The use of only AC will kill the fish!

To do the electrofishing there has to be both a certain voltage and power. How much of each depends on the content of ions in the water and the temperature of the water. When the conductivity is less it can be necessary with a higher voltage to archive effective electrofisheries (see figure 5).

Figur 5. The voltage drop in relationship to distance of the electrode in water with

different concuctivity.


As you can see on the figure, at very low conductivity almost all the voltage drop happens very nearby the electrode, which makes it difficult to do the electrofishing very effective. The other way about a raise in conductivity means that the voltage drop happens over a greater distance. But to hold the tension then, this demands a greater power (Watt).

When the temperature is lowered the conductivity drops.


The electricity field:

The electric field between the two electrodes will try to make a circular distribution around the anode. The voltage drop from this anode will decrease logarithmically with the distance. It means that there is a great voltage drop in the nearest metres of the anode and almost with no influence further away. You can say that it is the voltage drop just around the anode that will capture the fish…..

Because of the great voltage drop just around the anode, it is dangerous for the larger fish as the length of the fish will crucial for the voltage drop. When the fish swims into the electric field it reacts on the difference in voltage arising between the head and the tail (body tension).


The fish reaction in the electric field:

There are five different kinds of reactions (see figure 6);

  1. In the periphery of the electric field the fish is scared and swims away
  2. When the body tension is over a certain limit the body of the fish will start vibrate
  3. By increased body tension the fish will start swim against the anode
  4. If the body tension is raised increased even more, the fish will become anaesthetized and turn upside down
  5. Still increasing the body tension you will kill the fish 

Figur 6. The behavior of fish in the electrical field.


All this means that at the same distance from the anode the bigger fish will experience a greater body tension than the smaller fish and that it is relative easier to catch the bigger fish. 



The anode has to be circular and can be made from for example aluminium, cobber or stainless steel. To get an effective gentle electrofishing it is important that the diameter of the anode is as big as possible. This means about 30 cm when you do the electrofishing by foot, and about 60 cm when you do it by boat. The design of the cathode isn’t that important and it can be designed as a ring, a pipe or a frame. But the surface area is important and it is recommended that it is about three times as big as the surface of the anode.


Figure 7. The size of both the attraction and the immobilisation zone at

two different sizes of electrodes.

Practical fishing:

In small streams the electrofishing is done by walking against the flow of the water. Normally this will take three persons: One who is electrofishing, one who is holding the cable and dragging the boat and one is walking behind the boat and ready to turn of the electricity at the emergency stop.

The third person can also be holding one more net and be ready to shift out the net with the person who is electrofishing, if he catch a fish. In the boat there is a generator making the power and electricity and there is a tank to for keeping the captured fish. Remember to check the fish once in a while and see if you have to change some water so the water is oxygenated. Some people do the electrofishing by having a tank for the fish on land.

If you do electrofishing in a river you have to sail in a boat and often you will sail with the flow. It is a little bit more difficult and you have to use a generator with more power.

Usually it takes at least four people: One to hold the anode (electrofishing), one to sail the boat and two persons to catch the fish (one on each side of the person who is holding the anode in front of the boat). You have to figure out where the fish can be located, because in a wide river you will catch the most fish if you sail in one side of the river and not in the middle of the river.



Safety for the fish:

When you are electrofishing it is important to handle the fish with care. You are just “borrowing” the fish (and its reproduction system) and always remember that the fish should be restocked alive an in good condition.


There are some few rules that you have to follow:

  • Be careful when you are electrofishing; you can kill the fish by the electricity. Try to avoid to “hit” (affect) the same fish again and again.
  • The fish should be lifted out of the water as soon as it goes into the net. This for avoiding further influence from the electricity.
  • The net should be as big and easy as possible and be made by knotless mesh for the sake of the mucus of the fish.
  • You have to bring a big enough storage tank with soft edges so the fish wont hurt their mucus layer which will make them a lot more vulnerable to infection.
  • Avoid every non necessary handling of the fish which will stress the fish. Remember it is a wild animal which just by electrofishing is exposed to considerable stress.
  • Don’t lift the fish just holding it in the tail!!
  • During the electrofishing remember to exchange a lot of water so the fish will get some new oxygen.
  • You should avoid electrofishing, when it is freezing because you can damage the eyes of the fish.



Safety for you:

  • Always remember that you are working with electricity and water together, which normally is a bad combination!
  • Make sure that all the people, who are in the water, know what their role is and what they shall do if there should be an accident.
  • Make sure that the equipment is in good condition and that there is kept some services on it.


Always remember that it isn’t too late to learn some new stuff and that practical experience is a good thingJ

Used literature:


AK, October 1994: Electric current influence on fish. Ministry of Food, Agriculture and Fisheries.       Department for freshwater fisheries. 


Geerts-Hansen, Peter and Rasmussen, Gorm, 2002: Guide in Electrofisheries.


Poppe, Trygve, 1999: Fiskehelse og fiskesykdommer. Universitetsforlaget AS.


Sedgwick, Stephen Drummond, 1988: Salmon farming handbook. Fishing News Books Ltd. British Library CIP Data.


Vandkvalitet, version 03, 2001: DANAQ Consult, Billund Aquakulturservice.


Vandbehandling – Teori, version 03, 2001: DANAQ Consult, Billund Aquakulturservice.



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