This page is being edited and will be uploaded soon (October/November 2021).


The following section is an update of the basic introduction to RAS chemistry written by Dr. Bent Urup in 1997. 

This compact document provides the essential “Need to know – Chemistry” for those operating and making daily decisions within any RAS facility.

1) The basic principle of recirculation technology
2) Food and energy conversion in fish.
3) Chemical parameters in the RAS system.
4) Biofilter chemistry 


1) The basic principles of recirculation technology


Recirculated fish farms can be many things, but in general the idea is to reuse the water multiple times.

The higher level of water treatment, the greater the potential reuse of water. The optimal solution for a specific site depends on an economical evaluation, which will includes water availability, pumping heights/costs, water security, seaweed problems, management, optimal growth temperatures, etc.

But in locations with significant water temperature fluctuations indoor RAS systems with efficient water treatment technology create consistantly high growth rates by maintaining a constant temperature which is optimal for fish. This provides the basis for the return on investment in complex water treatment systems and is what is now considered a RAS farm.

In the simplest systems, water is simply repumped back to the tanks after re-oxygenation but no other treatment.

More sophisticated recirculation systems normally include mechanical removal of particulate material (food waste and faeces from fish), followed by removal of ammonia products, carbon-dioxide and re-oxygenation. Sometimes systems can also be supplied with bacteriological control such as UV treatment or Ozone.

Generally speaking, RAS fish production systems consist of fish tanks with water passed through a water treatment plant, where particles are removed, new oxygen is added, and other waste products are either removed or converted to a less harmful product, before water is returned to the fish tank (usually with the addition of some new water). The goal is to maintain water quality to facilitate healthy fish and optimal growth at minimum cost. However, when dealing with commercial production, investment and operation costs are key factors, and it is no just the goal to maintain the very best water quality possible. But a water quality which will make the fish perform well in the facility, stay healthy, and where the fish produced will be of a quality which will be desired by the costomers.

In conclusion, RAS aquaculture is about mass balances, securing a stable environment and installing technology to remove waste products at the same rate that they are produced by the fish.


2) Food and energy conversion in the fish

 Intro to water chemistry


Fig. 2.1


The values are of a general nature, as the actual values always depend on a number of actual production parameters including the fish species being farmed.

Typically feed contains approx. 50% protein. As protein contains 16 % of Nitrogen, feed contains approx. 8% Nitrogen. Fish contain approx. 3 % of Nitrogen by total wet weight.

The same considerations are applicable to Phosphor. The content of Phosphor in feed is typically in the range of 1 % while the Phosphor in fish is approx. 0.5% of wet weight. However, the phosphor of flatfish species (i.e. turbot) contains approx. 0.65% of wet weight.

The proportion of Nitrogen and Phosphor in feed not used to build new tissue in the fish is released into the surrounding environment. Figure 2.1 indicates that the major waste products are Phosphor, Nitrogen and Carbon-Dioxide.


  • Nitrogen

Nitrogen is primarily excreted by fish as Ammonia with approx. 80% excreted by the gills and the rest excreted in the faeces.

Ammonia excreted by the gills is un-ionised Ammonia - NH3, but due to the system pH level and the high pKa value of the NH3 – NH4+ buffer system, the majority is immediately converted to NH4+, which is significantly less toxic to fish, as it do not easily pass through the gill epithelia into the fish.

NH3 is quite toxic, and for most fish species, the level of NH3(N) should not be above 0.02 mg/litre in normal production conditions. However, higher levels have sometimes been seen in RAS systems without drastic effects but with reduced fish growth rates.

The problem with Ammonia in seawater is due to its high pH, see fig. 2.2 & fig. 2.3.  Any quick increase in pH within a production facility should be avoided.


Fig. 2.2

However, the NH3(N) equilibrium depends not only on pH, but to some extent salinity as well. Depending on source you will find small differences in measured amounts. See fig. 2.3a, 2.3b & 2.3c below.

 Fig. 2.3,a


 Fig. 2.3,b


 Fig. 2.3,c


  • Carbon-Dioxide

The second most important waste product is Carbon Dioxide excreted by the gills.

Fish use Oxygen to oxidise fat, sugar and proteins. As the carbon chains are broken down into free energy, carbon atoms are released as CO2.

Along with the complete breakdown of fat, approx. 0.71 mole of CO2 is produced per each used mole of O2. When proteins are the energy source, 0.8 mole of CO2 is produced per each mole of O2, When glucose is the energy source, 1 mole of CO2 is produced per each mole of O2.

In seawater and RAS farms in general, special attention must be paid to CO2 because of the water pH. However, it does depend on the chemical equilibrium with HCO3- and CO32-.



Fig. 2.4

In seawater the main part of CO2 is converted to HCO3-, which is less problematic for fish than CO2. However, it does inhibit the capacity of blood to transport CO2 from the tissues to the gills.

The non-spontaneous nature of the equilibrium between CO2 and HCO3- provides some benefits but also some disadvantages in sea water. In flow-through systems without, or with only a very limited reuse of water, CO2 is converted to the less harmful HCO3 with the CO2 diluted out of the system, without the CO2 reaching critical levels. This caused a misunderstanding in the early days of recirculation that CO2 was really not an issue in fish farming.

However, at higher levels of recirculation the accumulation of bicarbonate removal is difficult as only the CO2 fraction can be stripped out of the water system by normal means. This means that without an effective CO2 removal system at the same rate that CO2 is excreted by the fish, a slow build-up of CO2 to unacceptable levels will occur. Optimally, RAS systems should keep CO2 levels below 10-20 mg/l.

Dealing with the CO2/bicarbonate equilibrium has clearly been one of the biggest RAS technology challenges, especially for seawater, as the build-up of bicarbonate reduces the growth rate of the fish.

In discussing CO2 levels confusion can easily arise. We normally talk about free CO2 levels, which may not be the complete measurement that is needed depending on the technology applied. For example, equipment can be bought from Oxyguard which can measure levels of free CO2. However, it does not provide a measurement of the total amount of CO2, including the amount bound as bicarbonate, by titration. To calculate this fraction of CO2 the pH level must also be measured. In summary, a CO2 level measurement only make sense when taken together with a pH measurement.

Measuring free CO2 levels before and after a CO2 stripping, may indicate almost identical free CO2 levels even if the CO2 stripping process has removed nearly 100 % of the free CO2. This is because pH will have increased, as bicarbonate will have transformed back into free CO2. Therfore, in order to calculate the actual amount of CO2 removed, the sum is needed of 1) the difference in CO2 levels before and after the CO2 stripping and 2) the amount of CO2 regenerated from bicarbonate, which is determined by calculating the change in pH levels before and after the CO2 stripping.


  • Phosphorus


Some accumulation of Phosphor does not seem to be a problem for fish. In RAS systems where foam separators are applied, it can even provide some benefits in supporting foam creation. Regarding the discharge water from the system, Phosphor is often a key component of environmental permits. But it is relatively easy to reduce the Phosphor content of discharge water going into lakes, rivers and other freshwater environments where Phosphor is typically a limiting nutrient. By contrast, the discharge of Phosphor from RAS facilities into marine environments is not problematic and has very little impact as there are normally very high natural levels of Phosphor in marine environments.


  • BI5 - BOD

Biological oxygen demand (BOD) is a very important factor, and one of the reasons why it is important to effectively remove particulate matter in the mechanical filter. Per figure 2.1 removing particulate matter also removes Nitrogen and Phosphor. Hence, if particulate matter isn’t removed, it would have to be broken down biologically in the production water, causing consumption of O2 which would have to be replaced, and production of CO2, which would have to be removed. It is important to note, that the level of BI5 in the biological filter must be relatively low to convert Ammonia to Nitrate. Hence, the most effective way to make a biofilter work effectively is with effective mechanical filtration.

The introduction of effective high-capacity mechanical filtration systems was one of the most important break throughs for the development of RAS systems in the late 1980s. It dramatically increased the performance of biofilters, and it made it possible to avoid ecto parasite problems previously present in RAS and non-RAS farms. In summary, biofilter systems in RAS farms without efficient mechanical filtration, would have to be scaled 3-4 times larger which would then generate significantly more sludge and consume up to twice the amount of oxygen compared to a RAS system with a very efficient mechanical filtration system.



  • Oxygen


Fish use oxygen to oxidize food (see above under CO2). Oxygen can be added with new water which has a natural oxygen content, or by aerating the water either using air under pressure combined with diffusers at the tank bottom, or by using cascades, and pure oxygen (O2) injection. Pure oxygen is an efficient source which is typically required in intensive fish farms. But this tool which requires careful management, of CO2 levels as the addition of pure oxygen (instead of any form of aeration), does not remove CO2, which may be as problemic as a shortage of O2. At this stage of technological development, effective cascades with active v entilation, potentially under vacuum, are the most effective way to remove CO2 while providing effective aeration.

Some RAS systems use super-saturation of the production water. This should be avoided, or applied with care, as even small levels of super-saturation (110%+ oxygen saturation), can potentially reduce fish growth rates. While oxygen super-saturation can provide improved results in systems operated with high carbon dioxide/bicarbonate levels (as these parameters interact), keeping both parameters independently under control still yields far better results.


 Fig. 2.5


3) The chemical parameters in the system


  • Recommended general levels of compounds/parameters:


Ammonia (NH3):                                 < 0.02 mg/l**) (<0.05mg/l)

Nitrate(NO3-):                                     < 60 mg/l (NO3- - N)

Nitrite (NO2-):                                    <0.1-1 mg/l (NO2-   - N)*)

Carbon-dioxide(CO2):                        < 15 mg/l (30 mg/l)

Oxygen (O2):                                       70-110 % saturation.

Hydrogen Sulphide (H2S):                 < 0.001 mg/l

Chlorine residuals:                             < 0.001 mg/l

pH:                                                      6.9 -7.2 

*) Not very critical in seawater. During start of biofilter, levels of more that 8 mg/l can be found.

**) Some marine species may be less sensitive, levels up to 0.1 mg might be acceptable, but more experiments on each species are necessary. 

  • Metals – recommended max levels


Aluminium           (Al)                            < 0.06   mg/l

Cadmium            (Cd)                           < 0.005 mg/l

Chromium           (Cr)                           < 0.025 mg/l                                 

Copper                (Cu)                          < 0.005 mg/l

Iron                      (Fe)                          < 0.3     mg/l

Lead                    (Pb)                          < 0.01    mg/l

Manganese         (Mn)                         < 0.025 mg/l

Mercury               (Hg)                         < 0.0001mg/l

Nickel                  (Ni)                          < 0.005 mg/l

Zinc                     (Zn)                         < 0.025 mg/l




  • Water Chemistry parameters


i. Ammonia (NH3 – NH4+):

Waste product from fish metabolism. Even relatively small amounts of its un-ionised form, make it difficult for the fish to excrete Ammonia through the gills, which thereby makes even small amounts of Ammonia very toxic.


ii. Alkalinity:

Alkalinity is the sum of negative ions reacting to neutralize hydrogen ions when acid is added to water. Carbonate ions (CO3-) and bicarbonate ions (HCO3-) are the most important.  Alkalinity is measured in mg/l.

The alkalinity of seawater should be around 2 – 2.5 mg/l. Sodium carbonate (Na2CO3) can be used to adjust alkalinity.


iii. Carbon dioxide(CO2)

Carbon dioxide is produced by fish metabolic activity and bacterial breakdown of organic waste products in the system and influences oxygen uptake by fish. Levels above 20 mg/l should be avoided in the fish tanks, as higher levels reduce growth. Optimal levels should be below 10 -15 mg/l.


iv. Nitrate (NO3-)

Nitrate is formed by the nitrification from Ammonia to Nitrite and then to Nitrate and is not directly toxic to fish. Levels of less than 70 mg(N)/l does not seem to have a negative effect on most fish-species, and some RAS systems operate with levels up to 250 mg(N)/l (though these levels are known to be lethal to some fish-species).


v. Nitrite (NO2-)

Nitrite is an intermediary product in the nitrification process of Ammonia to Nitrate and is very toxic to fish, as it blocks haemoglobin’s Oxygen uptake in the blood. Levels of 0.15 mg/l have proven to be lethal in freshwater cases. In saltwater it is far less toxic, as salt seems to hinder or reduce the penetration of Nitrite through the gills. It is recommended to keep the level below 0.1 mg/l, though in some cases up to 1 mg/l or even higher can be acceptable. Any levels above 20 mg/l should be avoided even during up the start of biofilters.


vi. Oxygen

To provide optimal and even fish growth, Oxygen levels should at all times and in all tank areas be between 65% and 110% saturation. Oxygen levels should never fall below 60 % saturation in the fish tank.

If pure Oxygen is used, it should be noted that any super-saturation should be avoided as even levels of 110 % saturation will cause reduced growth, and levels of 160% can be directly lethal to some fish species.

The solubility of Oxygen varies with temperature and salinity see figure 2.5.

For optimal biofilter performance there should be above 4 mg O2/l even in the outlet. Oxygen levels below 2 mg risk the production of toxic compounds such as H2S. In this case, nitrification is considerabley reduced, and the level of Ammonia and Nitrite increases.


vii. pH:

pHs influences the toxicity of other chemical compounds and the uptake/release of Carbon Dioxide/Oxygen in the blood/tissue/gills of the fish.

From the nitrification process:


NH4+ + 1½ O2   → 2 H+ + NO2- + H2O


This process reduces pH by the production of H+.

Also, the production of Carbon Dioxide from fish metabolic activity and bacterial breakdown of organic waste products in the system, reduces pH if similar amounts of produced CO2 are not removed by CO2 stripping devises. See fig. 2.4


CO2 + H2O à H2CO3   → H+ + HCO3- à2H+ + CO32-


Due to natural buffers, a sufficient seawater exchange is normally enough to keep the pH within an acceptable range.

Different compounds can also be used to buffer or increase pH. Though sodium carbonate (Na2CO3) is often used, we do not recommend its use in seawater without carre. We prefer using NaOH (especially for seawater), when additional buffering is required (but only for the purpose of pH adjustment), though considerable care must be taken.


4) Biofilter chemistry


  • Biofilter

The purpose with the biofilter is to create an environment where a biological transformation of Ammonia products into Nitrate can take place, a process known as nitrification. As the necessary bacteria concentrate on surfaces, the biofilter consists of a tank containing material having a high surface to volume ratio. However, not only is the total surface area important, but also the distribution efficiency of the water containing the Ammonia to the surface of the filter material.

In the first part of the filter, organic material remaining after mechanical filtration is broken down through bacterial activity. This inhibits nitrification until the organic load is reduced to an acceptable level.

As the breakdown of organic compounds consumes Oxygen and produces Carbon Dioxide, some aeration / oxygenation is needed in the first part of the filter.

As heterotrophic activity in the filter may cause biofilm to build up on the biofilter media, it must be noted that nitrification is only effective when biofilm is very thin, preferably below 50 microns. Therfore, a visible biofilm indicates a misbalance in the biofilter and that the biofilter is not performing optimally.

Generally speaking, the nitrification process can be separated into two processes:


1)               NH4+ + 1½ O2    2 H+ + NO2- + H2O


2)               NO2- + ½ O2      NO3-


The first process is mainly carried out by a group of bacteria which during the early stages of RAS development was considered as Nitrosomonas.  However, it is now recognized that the process is more complex and may include many other bacteria species. Similarly, we consider that the second process in the biofilter is controlled by a group of bacteria dominated by Nitrobacter. Both groups are kemo-autotrophic, which means that they extract energy from the above chemical reactions, and mainly use the energy to build up carbohydrates from Carbon Dioxide.

Both processes require Oxygen, and in order for the biofilter to perform optimally, Oxygen saturation in the entire filter should be above 3 - 4 mg/l.

Levels below 2 mg/l pose risk anaerobic processes to take place, which can result in toxic compounds (more dangerous in seawater than freshwater due to the higher level of Sulphur which can create Hydrogen Sulphide (H2S)).

Separately, Hydrogen Sulphide is the reason that production water with high nitrate levels is discharged, denitrified in a separate water treatment process and is not allowed to be re-used via a return to the facility’s production flow. In its place fresh seawater is pumped in to replace the discharged water and continually dilute the production water to maintain acceptable nitrate levels. In other words, denitrification is only applied to the production water discharged from the RAS facility and is not allowed to return into the facility as this can cause fish mortalities.

Approx. 1g of Ammonia (NH4+) can be transformed into nitrate per m2 filter surface at 20 degrees. At 10 degrees the capacity will be reduced by approx. half which is reduced by half again at 5 degrees.

It has to be taken into account that the first part of the filter may not take part in the nitrification process (or have reduced capacity) due to organic load. This heterotrophic activity may require approx. 30% of the total filter capacity, even with mechanical filtration before the biofilter.

The doubling time at 10 degrees C. is approx. 20 hours for nitrobactor, and thirty hours for nitrosomonas. At 5 degrees C. the doubling time is approx. 40 and 80 hours respectively.

It normally takes approx. 3-5 weeks from first start-up for the biofilter to operate acceptably. At the beginning, high levels of Ammonia are seen followed by high levels of nitrite, before both levels drop to acceptable levels and a steady increase in nitrate is seen. See figure 4.1

 Fig. 4.1


The thinner the bacterial skin on the bio media, the more efficient the biofilter is. An old thick bacteria layer is inefficient and unpredictable. The biofilter typically works efficiently approx. five weeks after the first up-start, when it is in routine operation. Also the biofilter typically has its best performance approx. two weeks after each cleaning (for fixed bed filters).

Therefore, the operation of the biofilter requires establishing working routines to maintain efficient nitrification. This varies by fish-species, temperature, system set-up and other local conditions, so adjustments to the routine must be made per actual system performance.