The Marketplace is now widely available! Install insights today.
Download AppBlogFeaturesPricingSupportSign In

In addition to monitoring the general physico-chemical parameters that are important for maintaining water quality in aquaponic systems, and the biological parameters that indicate the system’s performance and reveal potential problems with water quality, it is also necessary to carry out regular check ups on the performance of the technology (filters, water, air pumps, etc.).


Solids removal

OPERATING PROCEDURE: A major consideration in aquaponics is the retention time and the removal of large particulate matter. These particles include uneaten food, fish waste, as well as other sources of biological material, such as plant particles. They can negatively impact chemical parameters such as pH and DO. Mechanical filtration (physical screens and barriers) will be the first important step in monitoring to enable the efficient removal of particulate matter. Visual inspection of the screens and filters is often the best method for checking for large particles. It is important that the particles are removed quickly, in order to prevent them from breaking down into smaller pieces, which would increase the time needed for them to be removed and would lead to increased oxygen demand due to an increased nutrient load (Thorarinsdottir et al. 2015). The screens should be cleaned frequently to ensure that the debris is removed.

MONITORING: For smaller particles, a useful measure is water clarity, otherwise known as turbidity, although this can be a subjective measurement, depending on the method used. The method is a representation of how well light is transferred through the water. The main cause of turbidity is often suspended solids, determined as total suspended solids (TSS). These can be measured accurately by dry weight. Firstly, around 1 L of water is taken from the system. The sample volume can be reduced for water laden with TSS, or increased if the water is clear. The water sample is then filtered through a pre-weighed filter paper of a specified pore size. Solids will remain on the filter paper, which can be weighed when completely dry (i.e. when the paper stops losing weight after continued drying). The increased weight of the filter paper provides a measure of the quantity of particulates present, which can be expressed in mg/L or kg/m3 (Rice et al. 2012) (Table 2).

Table 2: The procedure for measurements of suspendend solids

No.ProcedureRemarks1Weigh the filter paper to the nearest 0.1 mgRecord the mass as Mass 12Set up the filtration apparatus, insert a filter, and apply avacuum with a vacuum pump in order to draw the water through the filter3Wet the filter paper with a small volume of deionised (DI) water4Shake the sample vigorously and then measure out thepredetermined sample volume using a graduated cylinder.Record the volume filtered5Rinse the graduated cylinder and filter with three 20 mL volumes of DI water, allowing complete drainage betweenwashes6Continue suction with the vacuum pump for three minutes afterfiltration is complete7Carefully transfer the filter to an aluminium weighing dish, andplace the filter on a cookie sheet or similar device8Place the filters in an oven set to 104 ± 1 ⁰C, and dry for aminimum of one hour9Remove the filters from the oven and transfer them to a desiccator in order to cool them to room temperature. Weigh one sample filter to the nearest 0.1 mgRecord the mass as Mass 2 and apply the following equation: TSS(mg/L) = (Mass 1 – Mass 2) / Sample volume

TROUBLESHOOTING PROCEDURE: If it is found that large debris is accumulating on filters at rates which exceed the filters’ ability to remove them, an increased cleaning schedule should be implemented. If turbidity begins to increase, this can be a sign of a problem within the filtration system. Filters should therefore be checked regularly to ensure there are no blockages or, if possible, screen sizes should be reduced in order to capture smaller particles.


OPERATING PROCEDURE: Daily checks should be made on the mechanical function of the biofilter unit to ensure that the aeration system is functioning properly and that air bubbles are visible; this will ensure that there is a proper air supply for bacterial colonies. Light should be excluded from the biofilter, as this can encourage the algal growth; it should therefore be ensured that free water surfaces, i.e. above the fish tanks as well as at the plant unit, are covered with lightproof covers. Sludge may also build up on the biofilter media, so weekly checks should be made to ensure build-up is at acceptable levels, otherwise the efficiency of the system could be compromised.

MONITORING: The best way to monitor the functioning of the biofilter is by analysing the water for ammonia, nitrite, and nitrate levels, using specialised electronic or with photometrics tests to ensure that the water qualityis kept within optimal ranges for the target species, and to comply with national and EU legislation. These concentrations of ammonium, nitrite, and nitrate are usually measured using specialised electronic sensors since specific amounts create signatures in the conductivity of the water. The numerical readout can then be compared with the desired amounts. Another way of measuring levels of these nutrients is with photometrics tests.

TROUBLESHOOTING PROCEDURE: There are several steps which have to be taken if high levels of either ammonia or nitrite are detected. First, it has to be ascertained whether the biofilter has a suitable oxygen supply and is free from sludge. pH should be monitored closely, since nitrogen is converted to toxic ammonia (NH3) at higher pH levels and is especially harmful to fish. If pH is kept neutral or acidic, nitrogen is in the form of non-toxic ammonium (NH +) (see Table 3 in Chapter 5). The fish should then be starved for a few days to prevent increase in ammonium in the form of fish waste being added to the system. This will decrease the availability of ammonium, limit the growth of Nitrosomonas, and allow Nitrobacter colonies to convert excess nitrites into nitrates. Ammonia and nitrite may also compromise oxygen uptake in fish, therefore DO concentrations in the fish tanks should be kept optimal (Thorarinsdottir et al. 2015).

Formation of biofilms

OPERATING PROCEDURE: Not to be underestimated is the formation of biofilms, which can clog system components such as pipes or outlets or cause automatic sensors to take faulty readings. Therefore, biofilms should be checked and removed regularly (cleaning on a weekly basis is recommended).

TROUBLESHOOTING PROCEDURE: If, for example, only one sensor of the system displays a too low / too high value in the case of an oxygen alarm, it is possible that a biofilm has formed on the corresponding sensor, which leads to incorrect measurements. It has been observed that as the biofilm increases, the values for EC and oxygen continuously decrease. In case of an alarm, action must be taken immediately. It must not be assumed that the measurement is due to biofilm formation on the sensor.

Water and air pumps

OPERATING PROCEDURE: The mechanical devices that provide DO and flow have to be checked frequently (Table 3) to ensure proper functioning. Water pumps create a flow in aquaponic systems which transports nutrients and oxygen around it. They also move waste products towards the filters so that they can be removed. The misfunction of devices will result in decreased production. Without sufficient aeration, the fish and later also the plants will die. The check of the air pumps can often be done visually, by ensuring there is a steady stream of bubbles coming from the aerators. A reduction in DO may also be indicative of a problem. If problems occur, a suitably trained engineer should be sought to remedy the issue.

Table 3: Tasks related to an aquaponic system

Daily:Observe water flows at different system points in the aquaculture and the hydroponic unit (the water needs to circulate constantly)Verify the water pump interval; shorter interval = better water flowEnsure that the water pump is synchronized with the valves through which water enters the fish tanks and the hydroponic unitCheck that no overflows are clogged (for example by fish slurry, uneaten food or plant material, or by system parts)Seasonally:Check the functioning of the water pump and aeration systemClean the pump(s), aeration system, pipes, and the hydroponic unit if necessaryCheck the condition of the pipes and valvesCheck and regularly clean the pre-filter of water pumpsPeriodic replacement of membranes and wear parts in air pumps with membranes


Screens create a physical barrier between pumps, filters and, in some cases, the outside environment. Fish escaping from aquaponic systems can damage equipment, filters, and in extreme cases, can result in non-native species entering a natural ecosystem. It is important that appropriate locations for screens are identified. These will include pumps, input streams for filters, and pipes where water enters and exits the system.

OPERATING PROCEDURE: The screens should be checked daily for signs of wear and tear, and any damaged or worn screens should be replaced using suitable replacements.

Decoupling of the hydroponic of aquaponic compartment

In case of contamination in one system area, it is advantageous if the affected system part can be decoupled from the rest of the system easily (e.g. unplug a pump). This can be ensured by linking the hydroponic and aquaculture unit by, for example, a pump sump that connects the two system loops. It is important that all system components for water treatment are located on the aquaculture part, i.e. in front of the pump sump, so that appropriate water quality for the fish can be ensured.

TROUBLESHOOTING PROCEDURE: The main important application is that the fish can be saved if contamination occurs in the hydroponic section, for example due to improper use of pesticides. But it can also be advantageous the other way around, for example if fish need to be treated for disease with salt. . During the period of decoupling, the hydroponic system water can be fertilized with organic fertilizers, which certainly do not harm the fish (always remember that the two system loops should be linked together again as soon as possible).

Water quality

The term water quality includes anything that adversely affects the conditions required for maintaining healthy fish and plants. Maintaining good water quality in an aquaponic system is of extreme importance. Water is the medium through which all essential macro- and micronutrients are transported to the plants, and the medium through which the fish receive oxygen; therefore, it will directly affect the productivity and viability of the system. There are five key water quality parameters that are crucial for close monitoring in the system: DO, pH, water temperature, nitrogen compounds (ammonia, nitrites, and nitrates) and water hardness. Other parameters also need to be monitored in order to maintain a healthy balanced system, such as phosphorus and other nutrients, algae contamination, TSS, carbon dioxide concentration, etc. However, these parameters can be monitored less frequently in a well-balanced system (Somerville et al. 2014a; Thorarinsdottir et al. 2015).

Dissolved oxygen (DO)

DO describes the amount of molecular oxygen in water and is usually measured in milligrams per litre (mg/L). If DO levels are not sufficient, fish are under stress or suffer from slow growth, and could die. DO requirements differ for warmwater and coldwater fish. Bass and catfish, for example, which are warmwater species, require about 5 mg/L for maximum growth, whereas trout, a coldwater fish, requires about 6.5 mg/L of DO. High DO levels are needed by the nitrifying bacteria in the biofilter, which are essential for converting fish waste into plant nutrients. DO therefore indirectly affects plant growth as well. Also, plants need high levels of DO (> 3mg/L), which makes it easier for the plant to transport and assimilate nutrients across its root surfaces. Moreover, in low DO conditions, plant root pathogens may occur. It is recommended that DO levels be maintained at 5 mg/L or higher in an aquaponic system.

MONITORING: Oxygen levels should be measured frequently in a new system, but once procedures become standardised (e.g. proper fish stocking and feeding rates have been reached, and sufficient aeration is provided) it is not necessary to measure DO quite as often. Monitoring DO can be challenging because the measuring devices can be very expensive. There are some aquarium kits available that include reagents for testing DO content, but the most reliable approach is using DO probes with electronic meters, or online monitors that constantly measure the most significant parameters in the fish tank. In a small-scale unit it might be sufficient to frequently monitor fish behaviour, water, and air pumps instead. If the fish come to the surface for oxygen-rich surface water, this indicates that DO levels in the system are too low.

TROUBLESHOOTING PROCEDURE: Low DO levels are not usually a problem with hobby aquaponics growers using low fish stocking rates. The problem tends to arise more in operations with high stocking rates. If DO levels in your system are too low, increase aeration by adding more air stones, or by switching to a larger pump. There is no risk of adding too much oxygen; when the water becomes saturated, the extra oxygen will simply disperse into the atmosphere. Note that DO levels are closely related to the temperature of the water. Cold water can hold more oxygen than warm water, so in warmer weather, the monitoring of DO or preventively increasing aeration is essential.

Oxygen consumption is also related to the size of the fish: smaller fish consume considerably larger amounts of oxygen than large fish. This fact needs to be taken into consideration when setting up the system and stocking with small fish (Sallenave 2016; Somerville et al. 2014a). If low DO levels are detected in water in the hydroponic unit, this might be solved by installing an air pump.


The pH of a solution is a measure of how acidic or alkaline it is on a scale from 1 to 14 pH 7 is neutral, pH <7 is acidic and pH >7 is alkaline. pH is defined as the amount or the activity of hydrogen ions (H+) in a solution:


The equation shows that pH is lowered as the hydrogen ion activity rises. This means that acidic water has high levels of H+ and hence low pH. The pH of water is an especially important parameter for plants and bacteria. For plants, the pH controls the availability of nutrients. At a pH of 5.5-6.5, all nutrients are easily accessible for plants, but outside this range it becomes difficult (Figure 2). Even a slight pH deviation to 7.5 or above can lead to deficiencies of iron, phosphorus, and manganese in plants (see also Figure 10 in Chapter 5).


Figure 2: The impact of pH on nutrient availability for plants. By F. Moeckel [Public domain], from Wikimedia Commons

Nitrifying bacteria are unable to convert ammonia into nitrate at pH of 6 or below. This makes biofiltration less successful and ammonia levels may begin to increase. Fish have a pH tolerance range from about 6.0 to 8.5. In order to satisfy the needs of all three organisms (plants, fish, and bacteria), the pH in the aquaponic system should be kept somewhere between 6 and 7.

Certain events or processes in the aquaponic system will affect the pH, so it will not stay constant and will need to be regularly monitored. These processes are nitrification, fish stocking density, and phytoplankton contamination. In the nitrification process, bacteria produce small concentrations of nitric acid and the pH of the aquaponic system is lowered. Fish stocking density also affects the pH of the system. When fish respire they produce CO2 which is released into the water. Upon contact with water, CO2 is converted into carbonic acid (H2CO3), which also lowers the pH of water. This effect is greater at higher fish stocking densities. Phytoplankton is generally always present in aquaponic system, although high amounts are undesirable, because it competes with plants for the nutrients. Because phytoplankton photosynthesises, which uses up the CO2 in the water, this raises the pH, especially during the day when photosynthesis is at a maximum. All in all, aquaponic water generally acidifies and the pH will need to be regularly monitored and adjusted (Somerville et al. 2014a; Thorarinsdottir et al. 2015).

MONITORING: There are several methods for monitoring pH. The simplest is to use pH test strips, which is the cheapest method, but it is only moderately accurate. The next level of accuracy involves using water testing kits; however, the recommended and the most accurate method is to use digital meters with pH probes and on-line monitors for continuous monitoring. Ideally, the pH level should be monitored continuously or at least daily and properly adjusted.

TROUBLESHOOTING PROCEDURE: There are several ways to raise the pH in the system. The most common methods include:

  • Adding NaHCO3 whenever needed. Dissolve NaHCO3 in some water, add it gradually to the tank, and measure the pH. You might need up to 20 g per 100 L. Do not add too much at one time as this can kill the fish.

  • Adding strong bases, such as calcium hydroxide (Ca(OH)2), or potassium hydroxide (KOH). Dissolve the pellets or powder in water and add it gradually to the fish tank.

In some cases, the water in the system can be hard with a high pH, typically in regions with limestone or chalk bedrock. pH can also rise if there is a high evapotranspiration rate, or if the fish stocking density if not sufficient to produce enough waste to drive nitrification. In these cases, pH will need to be lowered by adding acid in the water reservoir prior the fish tank. In this case, phosphoric acid (H3PO4), which is a relatively mild acid, can be added to the reservoir water (never directly to the fish tank!) (Thorarinsdottir et al. 2015).

Water temperature

Water temperature affects all aspects of aquaponic systems. Each organism within the system has its own optimum water temperature range, which has to be considered when choosing the species of fish and type of crops. Moreover, a combination of fish and plants should be chosen that matches the ambient temperature of the system’s location, as changing the water temperature can be very energy-intensive. Temperature has an effect on DO as well as on the toxicity of ammonia; water contains less DO at high temperatures and more unionised (toxic) ammonia. High temperatures can also restrict the absorption of calcium in plants.

MONITORING: Water temperature can be monitored with analogue or digital thermometers, or with temperature probes. If using an on-line measuring device, temperature monitoring is usually included in the system.

TROUBLESHOOTING PROCEDURE: The water surfaces on the fish tanks, hydroponic units, and biofilters should be shielded from the sun by using shading structures. Similarly, the unit can be thermally protected using insulation against cool night temperatures wherever these occur. Alternatively, there are methods to passively heat aquaponic units using greenhouses or solar energy with coiled black hose pipes, which are most useful when the ambient temperatures are lower than 15 °C (Somerville et al. 2014a).

Total nitrogen (ammonia, nitrite, nitrate)

Nitrogen is a crucial water quality parameter. The sum of the un-ionised toxic form and the non-toxic ionic form of ammonia is called Total Ammonia Nitrogen (TAN). TAN is what most commercial ammonia test kits measure. In a fully functioning aquaponic unit with adequate biofiltration, ammonia and nitrite levels should be close to zero, or at most 0.25–1.0 mg/L (see Chapter 5).

OPERATING PROCEDURE: Water analysis for nitrogen compounds (TAN, NO -, NO -) should be performed daily or at least weekly in order to keep an eye on ammonium and nitrite peaks (Table 4).

Table 4: Parameters with target, maximal, and minimal values of nitrogen compounds in the system water

ParameterAbbr.UnitTarget valueLower thresholdUpper thresholdTotal Ammonia NitrogenTANmg/L0.0-1.0Nitrite-NO2mg/L0.0-0.2Nitrate-NO3mg/L0.0-300

MONITORING: Aquarium kits for measuring ammonia, nitrite, and nitrate are quite accurate and cost efficient. Spectrophotometric analysis can be used for more accurate measurement. There are spectrometric test kits available for measuring ammonia, nitrite, and nitrate.

TROUBLESHOOTING PROCEDURE: If nitrite or ammonia peaks occur, don’t feed the fish for several days, but do not stop feeding them completely as this will also starve the microorganisms in the biofilter (Klinger-Bowen et al. 2011) (see also the troubleshooting procedures for biofiltration in section 9.2.1).

Phosphorus and other nutrients

Nutrition plays a crucial role in plant health, and one method to check this parameter is by observing the condition of plant tissues by noting the overall condition of the plant. Changes in leaf shape and colour, as well as wilting of the plant, can be an indication of certain nutrient deficiencies, and prompt investigation will be needed to ensure the survival of the crop. The signs that plants may display if the presence of their most important nutrients becomes limited are described below. Optimal ranges of nutrients will differ from crop to crop, so it is therefore important that the operator is familiar with the optimal nutrient range for the chosen crop (Thorarinsdottir et al. 2015).

Phosphorus (P)

Deficiencies are characterised by poor root growth, reddening of the leaves, as well as dark green leaves and delayed maturity. The tips of plant leaves may also appear burnt (Thorarinsdottir et al. 2015).

Potassium (K)

Deficiency will cause lower water uptake and will impair disease resistance. Indications of potassium deficiency include burnt spots on older leafs, wilting, and the failure of flowers and fruits to develop properly (Thorarinsdottir et al. 2015).

Calcium (Ca)

Deficiencies are quite common in aquaponics, and signs include tip burn on leafy plants, blossom end rot on fruiting plants, and improper growth of tomatoes (Thorarinsdottir et al. 2015).

Magnesium (Mg)

Deficiencies usually involve changes in the colour of old leaves, with the area between the veins turning yellow, stiff, and brittle before falling off. It is rarely encountered in aquaponics (Thorarinsdottir et al. 2015).

Sulphur (S)

Deficiencies usually involve changes in the colour of new leaves, with the area between the veins turning yellow, stiff, and brittle before falling off. It is a problem rarely encountered in aquaponics (Thorarinsdottir et al. 2015).

Iron (Fe)

A lack of iron in a system presents itself visually, by turning the tips of the plants and the whole leaves of young plants yellow. This will eventually change to white with necrotic patches. A deficiency can easily be identified by noting changes to new leaves compared to old leaves. New leaves will grow and appear white, while old leaves will remain green. In order to facilitate uptake by plants, iron is often added in its chelated form, in concentrations of up to 2 mg/L. Iron can also be applied directly on leaves, with a spray. It is also important to monitor pH when iron deficiency is suspected, because at a pH below 8 iron may precipitate from water and prevent uptake by plants. A good rule to follow is to add 5 mL of iron per 1 m2 of cultivated plants. A high concentration of iron will not harm an aquaponic system, although it may give a slight red colour to the water (Roosta & Hamidpour 2011; Thorarinsdottir et al. 2015).

Zinc (Zn)

As a result of deficiency of zinc, the growth of plants will be stunted, presenting as shortened internodes and smaller leaves. Generally speaking, a major problem in aquaponics is zinc toxicity, because while plants can tolerate an excess, fish cannot and it can cause mortality. Zinc is used as part of the galvanisation process of fish tanks, nuts and bolts etc., and it is found in fish waste. Deficiencies are therefore rarely a problem. Levels of zinc should be kept between 0.03 and 0.05 mg/L, as most fish will become stressed at 0.1 to 1 mg/L, and will start dying off at 4-8 mg/L. As zinc is introduced to the system mainly through the coating on equipment, the best way to keep zinc levels within range is to use alternatives to galvanised equipment, such as stainless steel or plastic (Storey 2018) (for detailed information, see also Table 9 in Chapter 5).

MONITORING: Although monitoring plant tissues gives an indication of the nutrient status of the water, it only reveals itself after a deficiency has got to the stage that an issue has presented itself within the crop. The best solution is therefore consistent monitoring of water (see Water quality in 9.2.2.).

Water hardness

There are two types of water hardness, which are especially relevant for aquaponics: general hardness (GH) and carbonate hardness (KH). GH can essentially be described as the amount of calcium (Ca+), magnesium (Mg+) and, to a lesser extent, iron (Fe+) ions present in water. GH usually occurs naturally in areas where water courses flow through and into areas with high concentrations of limestone deposits. GH is important for both plants and fish within aquaponic systems, as Ca+ and Mg+ are essential plant nutrients and are therefore required for healthy plant production. It can also be a useful source of micronutrients for fish within the system; for example, Ca+ within the water can prevent fish from losing other salts, thereby increasing the overall productivity of the system.

KH is important primarily as a buffering agent. KH can be described as the total amount of carbonates (CO 2-) and bicarbonates (HCO -) within a system, which gives water alkalinity. KH therefore has an impact on pH levels, and acts as a buffer to increased acidity which can arise from certain physiological processes. For example, the nitrification process, which as previously discussed converts ammonium from fish waste into the nitrates used by plants, generates nitric acid as a by- product. This can build up and ultimately sufficiently decrease pH until it causes stress to organisms. H+ ions from acid added to the water will bind to carbonates (CO 2-) and bicarbonates (HCO -), buffering against increasing acidity (Sallenave 2016; Somerville et al. 2014a; Thorarinsdottir et al. 2015).

MONITORING: It is often not necessary to constantly monitor water hardness within a flow-through system if it is ensured that water input sources have adequate levels of GH to promote plant and fish health, as well as KH to neutralise the nitric acid built up during the nitrification process. The optimum hardness level (Table 5) for aquaponic systems is between 60-120 mg/L (moderately hard). In RAS systems, however, this should be monitored once a week. Water hardness expressed as milligrams of calcium carbonate equivalent per litre can be classified as:

Table 5: Water hardness classification based on corresponding concentrations of calcium carbonate

Water Hardness ClassificationConcentration (mg/L)Soft0-60Moderately Hard60-120Hard120-180Very Hard>180

Hardness can be measured using simple test strips. Total hardness can be measured in mg/L or °dH (degree of German hardness). pH will also give a measure of hardness, with more alkaline water being harder.

TROUBLESHOOTING PROCEDURE: If it is found that the water is not at a suitable level of hardness, it is often possible to fix this with additives to increase the level. Limestone or crushed coral can also be added to water to increase hardness (Sallenave 2016; Somerville et al. 2014a; Thorarinsdottir et al. 2015).

Algae contamination, settleable solids

Algal growth in an aquaponic system can have negative effects on its performance. Algae are photosynthetic organisms and will quickly and easily grow in water if exposed to light. Since they occur naturally in all sources of water, it is almost inevitable that they will occur within an aquaponic system. Algal morphology ranges from single celled organisms, known as phytoplankton, and multicellular types, known as macroalgae Phytoplankton can reproduce rapidly, turning water green, while macroalgae form long filamentous strands, which can attach to the bottom of tanks. Algal growth can affect the chemical characteristics of the water and can interfere with the mechanics of the filters and pumps. Algae compete with other organisms for nutrients. They produce oxygen during the day, and consume it at night. In serious cases, algal consumption of oxygen during the night can result in water becoming anoxic, causing fish death. Filamentous algae can also grow to quite large sizes, and are often tough to break down. This means that a build up of algae can cause damage to the filters and pumps which may be expensive to repair and which can compromise the performance of the system.

MONITORING: Monitoring algal growth is mostly simple, usually relying on visual inspection of the areas such as the walls of fish tanks, around pumps and filters, and around the roots of the plants.

TROUBLESHOOTING PROCEDURE: Algal growth can be prevented by blocking the light using screens (Somerville et al. 2014a).

Suspended solids can be categorised into settleable and non-settleable solids. Settleable solids are those which settle on the bottom of the fish tank. The largest contributor is fish solid waste, made up of faeces, uneaten food, and other biological material. It is estimated that 0.45 kg of fish feed produces 0.11-0.13 kg of solid waste (Sallenave 2016). Buildup of excess settleable solids will have a negative impact on an aquaponic system for several reasons. Firstly, the increased organic load will decrease DO as it decomposes. This will affect other organisms in the system, such as nitrifying bacteria which require oxygen in order to convert ammonia to nitrates. Secondly, particles can adhere to the plant roots, decreasing their efficiency.

MONITORING: To measure settleable solids, take 1 L of a well-mixed water sample, place it in an Imhoff cone (Figure 3), and leave for 1 hour to settle. The cone is graduated into mm, so a direct reading of mm/L can be directly inferred from the depth of settled material (MadeCivilEasy 2016).

TROUBLESHOOTING PROCEDURE: Settleable solids are removed by filtration, and it is therefore necessary to ensure that all the filters are of the correct size, and in good working order.


Figure 3: Imhoff cones for measuring settleable solids.

Plant health

Unfavourable conditions (e.g. suboptimal temperature, insufficient light intensity, nutrient deficiency, or pests and diseases) will decrease the overall performance of crops.

MONITORING: It is most important to ensure that parameters are set within the optimum range for the species and cultivars being grown.

TROUBLESHOOTING PROCEDURE: In such instances, close monitoring of the appearance of plants will help to identify the underlying cause (Somerville et al. 2014b).


One of the major benefits of aquaponic systems is the comparative resilience of plants to disease. Root rot is a disease which infects numerous species of plants growing in hydroponic systems. It has been shown, however, that crops grown in aquaponic systems have an increased resilliance to the causative agents, such as Pythium aphanidermatum (Stouvenakers et al. 2018).

OPERATING PROCEDURE: Operators should be diligent when it comes to monitoring for disease. A familiarity with the system is crucial in order to be able to observe any changes. Most important is the control of water quality and the physical parameters. Because of the controlled nature of aquaponics, it is possible to set parameters in such a way that the introduction and spread of disease are minimised.

MONITORING: For example, since root rot is only virulent at temperature ranges between 20-30 ⁰C, control of temperature is therefore an effective measure against its spread (Grosch & Kofoet 2003; Sirakov et al. 2016). Another important consideration is the microbial flora: beneficial bacteria and other microbes play an important role in plant health, so it is important that inoculants of these organisms are utilised, and their presence occasionally checked for using cultures; however, this is not easy and requires expertise.

TROUBLESHOOTING PROCEDURE: Plant health and leaf colour should be observed daily. Leaf shape can also tell us if a plant is doing well. Wilting and signs of stress can be useful indicators of plant health issues (root, collar, or vascular problems) as well as nutrient imbalances.

Relative humidity

Relative humidity can be described as the amount of moisture in the air, relative to the total carrying capacity of the air for water; for example, 75% relative humidity is equal to 75% of the total water content which could be present in the air. The level of water which air can hold is dependent on temperature, so a room at 30 ⁰C could have significantly more water than the same room at 25 ⁰C. The point at which relative humidity reaches 100% is known as the dew point.

OPERATING PROCEDURE: This parameter is an important consideration in aquaponics, because controlling humidity in a desired range can prevent disease, as well as fend off parasites. Like most organisms, parasites have an optimum threshold that they can efficiently operate under; for example, spider mites can cause damage to plants by puncturing the plant cells while feeding. As they cannot tolerate wet and humid conditions, misters are often used to increase humidity and prevent such damage being caused. Microorganisms such as mould and fungi can also cause an issue in aquaponic systems and as they are difficult to remove through filtration, humidity can be used to control spores (Brown 2006; Storey 2016). Some plant species are adapted to survive in humid conditions, while the converse is true of plants from more temperate regions. It is therefore important to understand what conditions best suit the plants that are being grown.

MONITORING: Once the optimum relative humidity for a crop has been established, it should be monitored constantly to ensure it does not fall outside this range for prolonged periods. Measuring humidity is a straightforward procedure, using a meter known as a hygrometer. This gives the relative humidity of an area as a percentage.

TROUBLESHOOTING PROCEDURE: If relative humidity falls outside of the desired range the temperature can be altered, as relative humidity is a function of temperature, and therefore if relative humidity is too low, an increase in temperature will allow water which has condensed to evaporate. Conversely, if humidity is too high, lowering the temperature will decrease the moisture in the air. One can also manipulate the airflow. Ventilation, for example, will dilute the water vapour in the air, thereby reducing humidity. There are also devices known as dehumidifiers which can be set to activate at a certain point to draw water out of the air. These can be especially useful in automating the process, thereby reducing operational costs (labour) (Brown 2006; Somerville et al. 2014b; Storey 2016).

Air temperature

Ambient air temperature will have an effect on how well plants grow. Most vegetables grow in the range between 18-30 ⁰C, though there are some species which are adapted to either higher or lower thresholds. Swiss chard and cucumbers, for example, will perform well between 8-20 ⁰C, while tropical species such as okra prefer temperatures between 17-30 ⁰C. Temperature can affect a plant’s ability to fend off disease, by causing stress, and by allowing pests and parasites to thrive. Another consideration is the plant’s physiological response to temperature. Leafy greens, for example, begin to flower and seed at higher temperatures, which affects their taste, making them bitter and unpalatable.

OPERATING PROCEDURE: It is important to consistently monitor the air temperature in an aquaponic unit, and the measurements should be taken at different locations.

MONITORING: It can either be done using a digital thermometer or with of an analogue thermometer. Any changes in temperature should be noted.

TROUBLESHOOTING PROCEDURE: If the temperature falls outside of the desired range, it can be increased or decreased using specialist equipment (e.g. air heaters, air conditioning units). The best way to ensure that the optimum temperature is kept throughout the year is to ensure that the cultured crop is adapted to the local climate (Leaffin 2017).

Light intensity

Under normal growing conditions, plants receive the light necessary for photosynthesis from the sun. Like other variables in nature, this depends on the geographical location, time of day, and local environmental conditions. Light is a fundamental requirement for plant growth, and therefore it is essential that the right levels are provided for the chosen crop, in order to ensure optimal yield (Chen Lopez 2018). Light may be measured by its intensity (lux), which is the number of photons reaching a surface of a defined size. The metric unit of light intensity is the lumen (lm), and lux is equal to one lumen per square meter. In aquaponics what is of interest is the number of photons reaching the surface of a leaf. Photons are a type of elementary particle, and are essentially packets of energy which make up a stream of light. The number of phototons trapped by a leaf is the determining factor in the rate of plant growth (Badgery-Parker 1999).

OPERATING PROCEDURE: Without the proper light intensity, plants cannot grow or perform as well as they should. The point at which photosynthesis is equal to respiration is known as the compensation point. This is the intensity that will allow plants to survive, but not to grow, and it differs from plant to plant. Conversely, the point at which light intensity does not increase photosynthesis, and therefore stops limiting growth, is known as the saturation point. Generally, the upper leaves will be saturated at around 32,000 lux. Due to shadowing, the lower leaves will not receive as much light as the upper leaves. In order for the whole plant to become saturated, the light levels need to be around 100,000 lux. Photosynthetically active radiation (PAR) is the part of the light spectrum which plants use for photosynthesis, and includes wavelengths from 400-700 nm, which represents almost all visible light (Badgery-Parker 1999; Chen Lopez 2018).

MONITORING: There are several ways of measuring light, and there are even apps which can be purchased for smartphones (although the reviews of these should be carefully checked, as they can sometimes be less than accurate). Because light intensity is based on its power, the energy used to power the lights can be extrapolated to give a measure of luminescence in watts, or watts per meter squared (Wm-2). Similarly, we can measure the amount of energy emitted from a source, such as a lightbulb, from a distance. A radiometer is a device that measures the power of a light source, and a pyranometer can be used to measure the total amount of short-wave radiation. Short-wave radiation includes photosynthetic light, as well as energy from UV and near infra-red (IR) light. Plants and people experience IR light as heat. These meters are cheap to purchase and use, although they do have their limitations, the biggest of which is that their use under electric lights can give erroneous readings, especially when the light source has high levels in the blue or red spectrum. Quantum sensors are a more accurate way of measuring light; however, they are more expensive than foot-candle meters. These are usually hand-held, battery-operated devices, which measure PAR. They display their reading digitally, and some come with data logging capabilities to enable the easy transfer of data to a computer. Thirdly, instruments measuring radiant flux, which is the amount of energy per unit of time, can be used to measure the intensity of light.

TROUBLESHOOTING PROCEDURE: As plant growth is not uniform, readings should be taken from different locations – dark and light – to ensure that there are no areas with severe deficiencies. If, for example, the lower parts of the plants are falling below optimum levels, then productivity will be reduced (Runkle 2009; Runkle 2012). Correcting light intensity when it falls below the optimum range is usually quite a simple process. If there are obvious issues, such as blown bulbs, these should be replaced. More lights can be added to areas which are darker, and the positioning of lights can be changed to ensure that all areas of plants receive the optimum level.

Fish health

Monitoring fish health is a central aspect of keeping a healthy aquaponic system.

OPERATING PROCEDURE: This is typically achieved through observation of the behaviour and physical appearance of stocks, and an understanding of what constitutes ‘normal’. To this end it is important to understand typical behaviour patterns and physical appearances of the fish species in question. Water quality plays an important role in fish health, and maintaining consistent good quality enables that the fish remain in a stress-free condition. Maintaining a healthy immune system will allow them to fend off complications arising from the introduction of disease and parasites.

MONITORING: Generally speaking, fish should be observed on a daily basis, and their condition, as well as any changes, should be noted; the clinical signs of stress, disease, and parasitic infestation.

TROUBLESHOOTING PROCEDURE: Another important consideration is stocking density and feeding rates. The potential introduction of stress and disease into a system, can be avoided by ensuring that the fish are kept at an appropriate stocking density, and that feeding is maintained at appropriate levels (Somerville et al. 2014c).

Feeding rates

It is important to monitor feeding rates for several reasons. Too much food can lead to an oversupply of nutrients in the water, resulting in complications in the chemical and micro(biological) parameters.

OPERATING PROCEDURE: Feeding fish too little can cause stunted growth, leading to decreased productivity in the system, as well as increased stress and aggression, which can cause fish to attack each other, resulting in wounds and sores which may become infected.

MONITORING: Typically, the quantity of feed is weighed, although the feeding rates can also be measured visually, by monitoring the fish until feeding rates decrease and they cease feeding; in some systems this is done using underwater cameras. Many fish feed companies will also give recommended feed rates, allowing operators to accurately estimate how much feed to give. Feeding rates should be observed and noted at each feeding to allow for monitoring.

TROUBLESHOOTING PROCEDURE: If feeding rates begin to reduce, this could be a sign that something is wrong in the system and appropriate action, such as investigation by a veterinarian, should be undertaken. An increase in feeding rates could be a sign that the fish are not being fed enough, in which case the feed should be increased (Masser et al. 2000).


Growth is an important measure of how well fish are doing in a system, and feed companies often provide growth charts which give an estimation of the expected growth rate of fish as a function of feeding rates.

MONITORING: Growth is measured physically, by first weighing and taring a suitably sized net on a hook scale. Fish are then caught using the net and both are weighed. Another way of weighing fish is to place them in buckets of water on a scale. This is especially practical if the fish are small, and more than one fish can therefore be weighed at the same time. Note that with this method, care should be taken as larger distressed fish can forcefully hit the sides of the bucket, thereby causing themselves damage. In order to measure the length of fish, it is generally advisable to anaesthetise them using a suitable anaesthetic, such as tricaine methanesulphonate. An appropriate amount of tricaine methanesulphonate is dissolved in a separate container of water, which is of a suitable size for the fish. The fish should be placed in the water until they become limp and safe to handle, and they can then be placed on a flat surface, measured using a ruler, and released. These measurements should be taken once a week and noted. Any unexpected change to size and weight should be investigated.

Indicators for assessing fish stocks

The most important indicators of healthy fish stocks are behaviour and physical condition. Anything out of the ordinary can be classed as clinical signs of disease, or stress.

MONITORING: Typically, fish should be monitored during and directly after feeding, and changes in the amount of food eaten should be noted. Healthy fish will exhibit some of the following behaviour (OIE 2018):

  • Swimming in an ordinary, purposeful way

  • Clean, intact fins, which are properly extended and utilised

  • Clear, clean skin, with intact scales

  • Not breathing at the surface of the water

Abnormal behaviour and clinical signs of problems within a stock are quite general, and it can be impossible to determine the cause of an issue based on these alone. Things to watch out for include (Bruno et al. 2013):

Behavioural signs:

  • Changes in feeding rates

  • Lethargy and morbidity

  • Changes in swimming patterns, such as flashing, spiralling, or failing to maintain buoyancy

  • Hanging around near water outlets

  • Hanging around at oxygen exchange points

  • Breaching the surface and gasping near the surface Clinical signs:

  • Shortened or flared opercula

  • Haemorrhaging

  • Exophthalmia (raised, popped out eyes)

  • Enophthalmia (sunken eyes)

  • Pale, zoned, or necrotic gills

  • Lesions

  • White patches

  • Inflamed vent

An ideal way to measure and record these signs is by way of a clinical score sheet, an example of which is shown in Table 5. A clinical score sheet is a sheet where clinical and behavioural signs can be recorded and noted, based on their severity – for example, weak, mild, and severe.

Table 5: An example of a clinical score sheet for recording clinical and behavioural signs in fish

Severe Mild Weak No sign Behaviour Moribund Lethargic Hanging vertical Spiralling Flashing Loss of equilbrium Body Dark Distended abdomen Anorexic Eyes Exophthalmic Enophthalmic Gills Pale Zoned Necrotic Lesions Flank Elsewhere


Stress can be one of the most damaging factors for fish in aquaponic systems. Alone, it may not be enough to kill stocks; however, chronic stress can lead to a number of complicating factors, usually caused by suppression of the immune system. Immunocompromised fish are more likely to fall victim to infectious agents, such as bacteria, viruses, and fungi, as well as parasitic infestations. It can also reduce a fish’s ability to counter sudden changes in its environment, leading to mortality.

MONITORING: Stress can be monitored directly in the organism, through the release of certain hormones, such as cortisol. However, this requires trained personnel, in order to ensure that no additional stress occurs. Such measurements also fall into the category of animal experimentation, and the local animal protection laws should be adhered to. The best way is to ensure that stressful situations are avoided. This can be achieved by ensuring that the fish are kept at the proper stocking density, fed appropriately, and that physical characteristics of the water (temperature, pH, DO, etc.) are kept at physiological optimums for the chosen species (Rottmann et al. 1992; Somerville et al. 2014c).


Disease is an important consideration in any system where animals are kept in higher stocking densities than would otherwise be found in nature, and this is also true of aquaponic systems. Issues involving disease can be exacerbated by poor conditions, such as low DO, and can also cause opportunistic pathogens to introduce infection.

OPERATING PROCEDURE: Generally speaking, contained recirculating systems are somewhat insulated from the introduction of the causative agents of disease. This can be a double-edged sword, however, as it may be difficult to eradicate disease following its introduction, and the sooner that issues are identified, the more effective treatment and remedial action will be. In flow-through systems, filtration through sand, for example, or treatment using UV light can all reduce the likelihood of the introduction of disease. In either case, careful and consistent monitoring is necessary. Even with careful prevention, it is possible that disease may be introduced to the system, and it is important that this is recognised and addressed with the aid of veterinary advice, if necessary.

MONITORING: In order to appropriately monitor stocks, it is important that operators are familiar with clinical and behavioural signs which fish may exhibit and are identified above. In a system with a high number of animals, it is likely that there will be instances of fish which are poorly, and while it may not be indicative of a disease, it is recommended that daily checks are carried out in order to monitor the overall health of the stock and mortalities; dead fish should be removed from the system and disposed of in a bio-secure manner. If the frequency of clinical signs or mortalities begin to increase, it is important to ensure that procedures are in place to first identify the issue and then take remedial action.

TROUBLESHOOTING PROCEDURE: For this reason, it is important that operators are aware of how to contact a veterinary specialist in fish health (Martins et al. 2010; Somerville et al. 2014c).

Parameters of special interest

Sometimes non-standard parameters in water quality will become relevant in an aquaponic system, especially when choosing the source of your water. You can choose to use water from the environment (rain water, river or lake water, etc.), or municipally treated tap water. Depending on the water source, the water may differ in the levels of DO, presence or absence of heavy metals and other micropollutants, trace chemicals, and disinfectants, and it may or may not be contaminated with coliform bacteria. The water that is added to the system can be of a very different quality depending on:

  • The location of source water

  • The recent weather (if using water from the environment)

  • Municipal water treatments (if using tap water)

OPERATING PROCEDURE: Drinking water treatment often includes the addition of disinfectants, such as clorine and chloramines. These must have a residual effect, which means they remain active in the water after application of the disinfectant. This can be problematic in an aquaponic system, since it relies heavily on the microbial communities in the biofilter. On the other hand, water taken directly from the environment can have other issues, including contamination with undesirable microbes, such as coliform bacteria, or the presence of pollutants, such as endocrine disrupting chemicals and heavy metals (Godfrey 2018).

MONITORING: Monitoring of these non-standard parameters is impossible without access to analytical techniques such as high-performance liquid chromatography (HPLC), inductively coupled plasma mass spectrometry (ICP-MS), atomic absorption spectroscopy (AAS), and microbiology lab equipment and materials, such as an incubator, laminar flow hood, autoclave, vacuum filtration apparatus, and microbiological growth media. Since this equipment is very expensive, it is best to consult a national laboratory for specific measurements if a problem with source water is suspected.

TROUBLESHOOTING PROCEDURE: A more economical and practical solution is to avoid problems with the source water altogether by installing a carbon filter, which will remove any disinfectant residues and potential pollutants, and a UV filter which will deactivate any unwanted microbes in the source water.

Copyright © Partners of the [email protected] Project. [email protected] is an Erasmus+ Strategic Partnership in Higher Education (2017-2020) led by the University of Greenwich, in collaboration with the Zurich University of Applied Sciences (Switzerland), the Technical University of Madrid (Spain), the University of Ljubljana and the Biotechnical Centre Naklo (Slovenia).

Please see the table of contents for more topics.

[email protected]

Stay up-to-date on the latest Aquaponic Tech


  • Our Team
  • Community
  • Press
  • Blog
  • Referral Program
  • Privacy Policy
  • Terms of Service

Copyright © 2019 Aquaponics AI. All rights reserved.