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Water Quality / Bioremediation

Parameters, problems, troubleshooting and tips

Water quality is of utmost importance in fish and shrimp farming. Regardless of the particular aquaculture system used, maintaining balanced levels of water quality parameters is fundamental for both the health and growth of farmed aquatic species.  

Here we examine water quality parameters that matter most to aquaculture producers, and look at best practices when it comes to monitoring and adjusting these levels.  

Table 1 provides an overview of key water quality parameters listed by importance, along with standard values, recommended measurement frequency and measurement procedures. 

Table 1. Water quality parameters, measurements and preferred ranges for aquaculture | Source: BIOMIN

ParameterStandard valuesFrequency of measurementMeasurement proceduresImportance of
parameter to be measured
Dissolved oxygen> 4.0 mg/l> Twice dailyTitrimetric, colorimetric, probe+ + +
TemperatureSpecies dependent

> Twice daily

Thermometer, probe+ + +
pH7.5 – 8.5

Twice daily

Colorimetric, probe+ + +

Freshwater: < 0.5 ppt

Brackishwater: 0.5 – 30 ppt

Saltwater: 30 – 40 ppt

Optimum: 15 – 25 ppt

Refractometer, conductivity meter,

+ + +
Ammonia (NH4+/NH4-N)0 – 0.5 ppm2-3x weeklyColorimetric, probe+ + +

Freshwater: 30 – 5000 μSiemens/cm

Saltwater: 50000 – 60000 μSiemens/cm
-Conductivity meter+ +
Nitrite (NO2-)< 1 ppm

2-3x weekly

Colorimetric+ +
Alkalinity50 – 300 ppmMonthlyTitrimetric+ +
Phosphorus (P)< 0.5 mg/l-Test kit+ +

Nitrate (NO3

< 100 mg/l

2-3x weekly

Hardness40 – 400 ppm-Titrimetric+
Redox Potential+125 to –200 mV-Methylene blue, Redox meter+
Hydrogen sulfide (H2S)0 ppm-


Carbon dioxide (CO2)< 10 ppm-Titrimetric+

Biological oxygen demand

< 50 mg/l-Conductivity meter+
Turbidity or Total dissolved solids (TDS)Site dependent-Sechii disk, probe+
Tip: Use a multiparameter probe for water quality testing 

Aquaculture specialists and producers need special equipment to ensure good water quality in their systems. Besides basic test strips, a multiparameter water quality meter or probe is a fast and easy way to obtain reliable water quality data. It works simply by submerging the sensor into the pond water. 

Dissolved oxygen 

Dissolved oxygen (DO) is one of the most important parameters in aquaculture. Maintaining good levels of DO in the water is essential for successful production since oxygen has a direct influence on feed intake, disease resistance and metabolism.  

A sub-optimal level of dissolved oxygen is very stressful for fish and shrimp. Lower levels e.g. 3 ppm of dissolved oxygen result in slower growth and decreased immune response and levels below 1 ppm can be lethal. It is therefore important to keep dissolved oxygen levels in aquaculture systems above 4 parts per million (ppm). 

Effects of DO concentration on shrimp (adapted from Lazur, 2007) | Source: BIOMIN
Effects of DO concentration on shrimp (adapted from Lazur, 2007) | Source: BIOMIN
Oxygen cycle and aeration 

The dynamic oxygen cycle of ponds fluctuates throughout the day due to phytoplankton photosynthesis and respiration. Managing the equilibrium of photosynthesis and respiration – as well as the algae growth – is an important task in the daily work of a farmer.

Maximum DO will occur in the late afternoon due to the build-up of oxygen (O2) during the day through photosynthesis.As phytoplankton (microscopic algae) usually consumes the most O2 and since photosynthesis does not occur during the night, DO levels decline. 

Critically low DO occurs in ponds specifically when algal blooms crash. The subsequent bacterial decomposition of the dead algae cells demands a lot of oxygen. It’s important to note that the DO concentration in water goes up as temperature goes down, and decreases when salinity increases. 

When feeding the fish and shrimp, oxygen demand is higher due to increased energy expenditure (also known as specific dynamic action). To face this higher oxygen demand, several measures can be taken. 

Figure 3. The daily oxygen cycle in a pond | Source: BIOMIN
Figure 3. The daily oxygen cycle in a pond | Source: BIOMIN
Oxygen diffusion - aeration 

Other sources of oxygen than photosynthesis are diffused or transferred from air to water. Wave action or mechanical aeration forces this oxygen diffusion. Paddlewheel aerators accomplish this by breaking water into small droplets and increasing the contact between the water surface and air. Aspirator aerators compel air into the water through a venture and a propeller.  

How to measure dissolved oxygen 

In intensively cultured ponds, it is recommended to use a probe to assess dissolved oxygen at least twice a day. Results are presented either in mg per liter (mg/L) or parts per million (ppm). 0 ppm refers to total oxygen depletion and 15 ppm to the maximum or saturated concentration.  

In order to get the maximum and the minimum levels, measurements should be made one hour before sunrise (± 30 min) and two hours before sunset (± 30 min). When a pond is in “equilibrium” the DO level will not change drastically. The frequency of monitoring should be increased when the DO drops below 4.0 mg/L.

How to increase dissolved oxygen in a fish or shrimp pond 

A sub-optimal dissolved oxygen level is the major limiting water quality parameter in aquaculture systems. Fortunately, there are a number of actions you can take to improved dissolved oxygen levels in your operation.  

  1. Use aerators during the night time when dissolved oxygen falls below 4 ppm 

  2. Flush out decaying plankton when plankton die-off occurs and provide additional aerators and aerate for additional hours 

  3. Reduce the feeding rates or have the same feed spread over more frequent feeding 

  4. Circulate the pond water to avoid temperature differences 

  5. Exchange water (in addition to aeration) to improve low dissolved oxygen values 


Water temperature can affect fish and shrimp metabolism, feeding rates and the degree of ammonia toxicity. Temperature also has a direct impact on biota respiration (O2 consumption) rates and influences the solubility of O2 (warmer water holds less O2 than cooler water). 

Temperature cannot obviously be controlled in a pond. Aquatic animals modify their body temperature to the environment and are sensitive to rapid temperature variations. For each species, there is a range of temperature conditions.  

SpeciesLower lethal temperaturePreferred temperatureUpper lethal temperature
Rainbow trout013-1724-27
Nile tilapia8-1231-3642
Tra catfish923-2733
Crucian carp025-3238
Channel catfish922-2937
Tiger prawn1425-3036
White shrimp14>2040

Table 2. Temperature (°C) conditions for aquatic species | Source: BIOMIN

It is therefore important to adapt fish and shrimp progressively when transferring them from tank to pond. It’s important to note that every 10 °C increase in temperature doubles the rate of metabolism, chemical reaction and O2 consumption. 

How to measure water temperature 

Temperature should be measured on-site twice a day, generally between 5am and 7am and 1pm to 3pm using a thermometer or probe. Temperature differences should not be considerable, since temperature has a direct effect on growth, O2 demand, food requirements and food conversion efficiency. 

pH water quality  

pH is a measure of acidity (hydrogen ions) or alkalinity of the water. Optimal pH levels in the aquaculture systems should be in the range of 7.5 – 8.5. 

It is important to maintain a stable pH at a safe range because it affects the metabolism and other physiological processes of fish and shrimp. Values outside of that range can create stress, enhance susceptibility to disease, lower production levels and cause poor growth and even death.  

Signs of sub-optimal pH in an aquaculture pond:  

  • Increased mucus on the gill surfaces of fish 
  • Unusual swimming behavior 
  • Fin fray 
  • Harm to the eye lens  
  • Poor phytoplankton and zooplankton growth 

Variables related to pH 

At higher temperatures, fish and shrimp are even more susceptible to pH variations. The CO2 concentration in the water also influences the pH, e. g. an increase in CO2 decreases the pH.  

As phytoplankton in the water utilizes CO2 for photosynthesis, the pH will vary naturally throughout daylight hours. pH is generally lowest at sunrise (due to respiration and release of CO2 during the night) and highest in the afternoon when algae utilization of CO2 is at its greatest. Waters of moderate alkalinity are more buffered and there is a lesser degree of pH variation. 

Figure 4. CO2 and pH correlation influencing the toxicity of NH3 | Source: BIOMIN
Figure 4. CO2 and pH correlation influencing the toxicity of NH3 | Source: BIOMIN
How to measure pH  

For routine maintenance, pH readings should be taken and recorded regularly using colorimetric analysis or a multiparameter probe. The measured pH level will be influenced by the time of the day the sample is taken due to fluctuations of the CO2 level.  

Therefore, pH should be measured before dawn for the minimum level and in the afternoon for the maximum level. A sudden drop of more than 0.5 indicates that the water in the tank should be partially changed. 

How to lower pH in ponds 

Different management strategies can be used to decrease high pH and minimize the risk of pH toxicity to freshwater fish and crustaceans.  

The method of choice should be based on specific needs and can be combined to be more effective.  

  1. Add sodium bicarbonate (NaHCO3) to neutralizes acids and bases. However, this requires large amounts since NaHCO3 is a weak acid. 

  2. Fill and prepare ponds several weeks before stocking. Start stocking after the initial flush of algae growth. 

  3. Reduce feeding rates to decrease nutrient input or have the same feed spread over more frequent feeding. 

  4. Add gypsum (calcium sulfate CaSO4) as soon as the pond is filled to balance hardness and alkalinity.  

  5. Apply aluminum sulfate (AlSO4) which forms an acid, removes algae and phosphorus. An initial dose of 10 mg/L with additional applications in 5 to 10 mg/L increments is recommended. 

  6. Reduce algae growth by adding herbicides, but only to change one type of plant community to a more desirable type (e. G. from filamentous algae to phytoplankton). A safer option is to reduce the amount of sunlight (e. g. add an aquaculture dye or keep the pond water turbid by aerating). 


Salinity represents the total concentration of dissolved inorganic ions, or salts, in water. It plays a significant role towards the growth of cultured organisms through osmoregulation of body minerals from that of the surrounding water.  

For better survival and growth an optimum range of salinity should be maintained in the pond water. If salinity is too high, fish and shrimp will start to lose water to the environment. Younger shrimp appear to tolerate a wider fluctuation of salinity than adults. Drastic changes in salinity may also alter the phytoplankton fauna and their population densities and lead to instability of the ecosystem. 

How to measure salinity 

It is recommended to monitor salinity daily. Measurements of salinity can be performed with the conductivity meter and are expressed in mg/l or ppm.  

Standard values for salinity | Source: BIOMIN 

Water type

Value in parts per thousand

Fresh water

< 0.5

Brackish water

0.5 – 30

Salt water

30 – 40


15 – 2


Ammonia matters a great deal to fish and shrimp production.  

Toxic ammonia comes from major waste products of shrimp and fish and uneaten feed. High levels occur most likely in summer when feeding rates, water temperature and pH are high and when algae population is low. It causes stress, gill damage and poor growth when the concentration is > 2.0 mg/l. At more than 2.0 mg/l ammonia causes death of shrimp and fish.  

Keeping ammonia levels in ponds below 0.5 ppm is important. To avoid an accumulation of ammonia, preventive measures must be taken through optimum feeding rates, maintaining healthy algae blooms and water exchange.  

Ammonia in water exists in two forms, as ammonium ions (NH4+), which are nontoxic, and as the un-ionized toxic ammonia (NH3). The relative proportion of one or the other depends on water temperature and pH.  

The higher these are, the greater the concentration of the toxic form. The sum of both, the ionized and un-ionized form, is the total ammonia nitrogen (TAN) which is usually measured by chemical test kits.  

The ammonia concentration in the pond can also be calculated by measuring TAN, temperature and pH. 

Table 3. Percentage of TAN in NH3 at different temperatures and pH levels (adapted from Boyd, 1982) | Source: BIOMIN
 8 °C12 °C16 °C20 °C24 °C28 °C32 °C

For example: Water at pH 8.0, 24 °C and 3 mg/l of TAN (sample measured) contains 5.0 % NH3 (from Table 3). Therefore, 3 mg/l x 5 % / 100 = 0.15 mg/l NH3. 

Note: If the phytoplankton absorbs too much CO2 during the day, and therefore the pH increases the pH to a value above 8.5, the fish and shrimp are subjected, depending on the total ammonia nitrogen concentration, to high NH3 concentrations. 

How to reduce ammonia in fish and shrimp ponds 

If high levels of ammonia are present within the pond water, a number of measures can be taken.  

  1. Reduce or stop feeding since high feeding rates lead to eutrophic conditions characterized by substantial phytoplankton blooms 

  2. Flush the pond with fresh water

  3. Aerate the pond, since low oxygen concentrations increases the toxicity of ammonia.  

  4.  Fertilize the pond with sources of carbon such as molasses, flour, starch, etc. to increase the carbon-nitrogen (C:N) ratio. 


Nitrite (NO2-) is another form of nitrogenous compound that results from feeding and can be toxic to shrimp and fish. Nitrite is an intermediate product of the transformation of ammonia into nitrate (nitrification) and nitrate into nitrogen gas (denitrification) by bacterial activity. The absorbed nitrites from the gut bind to hemoglobin and reduce its ability to carry oxygen. 

Note: An increase in CO2 may decrease the pH to a value below 6.5, which can lead to toxicity of nitrite through the formation of nitrous acid (HNO2). 

Regular testing of the nitrite concentration is essential. The nitrite test kit measures nitrite ions in fresh- and seawater. At 2 ppm (mg/l) and above, nitrites are toxic (injurious or lethal) to many fish and shrimp 

Figure 5. Nitrification and Denitrification (adapted from Hagenbuch, 2007) | Source: BIOMIN
Figure 5. Nitrification and Denitrification (adapted from Hagenbuch, 2007) | Source: BIOMIN

What is nitrification? 

Nitrification is the biological oxidation of ammonia with oxygen into nitrite followed by the oxidation of these nitrites into nitrates. AquaStar® Pond and AquaStar® PondZyme contain a Paracoccus strain, which is able to degrade ammonia in an organic material-rich environment, such as the pond environment. 

What is denitrification? 

Denitrification is the conversion of nitrate to gaseous compounds (nitric oxide, nitrous oxide, and N2) = NO3- degradation by bacteria. They complete the nitrogen cycle through the return of N2 to the atmosphere.  

Denitrification occurs in both soil and aquatic conditions, when there is supply of oxidizable organic matter, reducible nitrogen sources and low oxygen, such as in pond waters. Denitrifying bacteria include the Bacillus and Paracoccus species contained in AquaStar®.  

Autotrophic denitrifiers (e. g. Thiobacillus denitrificans in AquaStar® Pond and AquaStar® PondZyme), which obtain their energy from carbon dioxide or inorganic compounds, have also been identified. 

Alkalinity and hardness 

Alkalinity is the buffering capacitiy of water and represents its amount of carbonates and bicarbonates. Hardness refers to the concentration of calcium and magnesium in water. Alkalinity can affect the potential for primary productivity and also the water pH.  

Optimum hardness and alkalinity levels for aquaculture are in the range of 50 - 300 ppm CaCO3, which provide a good stabilising effect to pH swings. The sample is determined with standard test kits.  

Values of 50 – 100 mg/l are generally considered moderate for fresh water farming. To keep a balanced shrimp farming system, alkalinity values are recommended to be above 100 mg/l. Total alkalinity has been traditionally expressed as milligrams per liter (ppm) of equivalent calcium carbonate (CaCO3).  

Generally, alkalinity varies from site to site. In seawater, alkalinity is normally higher than 100 ppm but in freshwater areas, alkalinity is often low, particularly during the rainy season. Low alkalinity in freshwater or in low salinity areas will affect the survival rate and molting of shrimp. 

Waters can be classified by the degrees of hardness.  

CaCO3 mg/l


0 - 75


75 - 150

Moderately hard

150 - 300


Above 300

Very hard

Hard waters have the ability to buffer the effects of heavy metals such as zinc or copper which are toxic to fish and shrimp. Thus, hardness is a crucial parameter in maintaining good pond balance. Water alkalinity and hardness can be enhanced by liming ponds. Lime can be used to reduce the acidity in water. In case the water pH fluctuates greatly during the day, lime can also be used to increase alkalinity in the water to stabilize the water pH. However, there is no practical way to reduce alkalinity and hardness. 



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