How to Troubleshoot Your Aquaponics System

Aquaponics system problems are common, as growers face issues occasionally. However, by being aware and understanding the problems your aquaponics system is facing, you can have an advantage in addressing them before they even arise. This post will help you troubleshoot issues you might encounter during your aquaponics journey. 

If you encounter any issues with your aquaponics system, the first step is to check the water pumpair pump, and pipes to see if there are any leaks. The next step is to check the water quality. Understanding the water quality will provide the feedback essential for determining how to solve the issue. Below is a list of the common problem most aquaponics growers encounter when running their system and how to troubleshoot them. 

Electricity, Pipes, Pump and Air Pumps Problems





1. Electricity is off. The pumps are not working.

No electric power

The dissolved oxygen will decrease

1. Install a backup power system if the electricity supply is unreliable.

2. Install a container above the fish tank to release a slow stream of water into the fish tank to create bubbles. Repeat the process when the container runs out of water until power returns.

2. Electricity is on. The pumps are not working.

Faulty, broken or clogged pump

Broken or clog pumps. DO will decrease.

1. Check the pipe and replace it immediately if it is faulty. 

2. Check and clear any obstructions in the pipes.

3. Unusually low water or slow movement of water

Leaking or cracked pipes

Cracks, leaks, or clogged pipes

1. Fix any leaks or holes. 

2. Replace cracked or leaking pipes to prevent the fish tank from losing water. Replenish the water. 

Water Quality Test in Aquaponics

Water Quality Problems





1. Ammonia > 1 mg/liter

1. Not functioning bacteria

2. Too many fish

3. Accumulated waste such as uneaten food, dead fish, and other solid wastes

Fish stress or death

1. Change ⅓ -½ of the system's water with new water immediately

2. Remove solid waste such as unwanted fish food or dead fish

3. Stop feeding until the ammonia level decreases

4. Check and ensure the pH level is at its ideal range

5. Check your component's ratios, such as biofilter size and feeding routine

2. Nitrite is > 1mg/liter

1. Not functioning bacteria

2. Too many fish

3. Accumulated waste, such as uneaten food, dead fish, and other solid wastes

Fish stress or death

 1. Add 1 g of salt for every liter to neutralize the toxic water quality threat and then change the entire water volume of the system over two weeks

    3. Carbonate hardness (KH) is 0 mg/liter.

    The acid created in the system uses carbonate

    The pH in the water will change, stressing the fish and plants

    Add calcium carbonate to the system

    4. Water temperature is too low (<15 °C) or too high (>33°C)


    1. The fish will stop eating, and plants will wilt if the temperature is too high.

    2. The fish will stop eating, or the bacteria will stop working if the temperature is too low. 

    1. Shade the system during summer to ensure the temperature remains cool

    2. During winter, cover and insulate the system and use heaters

    3. Reduce feeding.

    4. Reduce plants

    5. Change fish and plants into species that are suited to the climate

    Plant Problems





    1. Plants are not growing, or the leaves color is changing

      1. Plants are deficient in some essential nutrients

      2. Plant diseases

      3. Too high temperature for the plants.

      1. Plants don’t grow or do not produce fruit.

        1. Ensure the water quality is optimum for plant growth.

        2. Check for nutrient deficiency in plants,

        3. Check if the nitrate level is too low, and increase the feed slowly if it's too low.

        4. Add aquaponics-safe fertilizer if necessary.

        2. Some plants are thriving, while some are not

        Uneven distribution of nutrients

        Uneven growth of plants in the grow bed

        1. Ensure that water is distributed evenly in the grow bed by using an irrigation pipe with small holes

        2. Check the nitrate levels

        3. Ensure the lines are clear

        3.Nutrient Deficiency in Plants

        Here is a table for identifying and correcting nutrient deficiencies in aquaponics plants. For more information on nutrient deficiency in aquaponics plants, click here

        Nutrient Deficiency




        Stunted plant growth, light green upper leaves, and yellow lower leaves.

        Add more fish


        Stunted plant growth and darker leaves

        Add rock phosphate


        Yellowing on the tips and edges of younger leaves, developing dead or yellow patches on the leaves, curling of leaf tips

        Add potassium hydroxide, potassium sulfate, or kelp meal concentrate 


        Pale leaf edges or edges have cup-shaped folds. 

        Use Epsom salts as leaf spray.


        New leaves are yellow and white

        Use chelated iron


        New leaves are misshapen or stunted, drying on the tips of the leaves

        Spray calcium chloride mixed with water or using hydrated (agricultural lime).

        Fish in Aquaponics System

        Fish Problems





        Fish are piping at the water surface

        Too low oxygen level.

        Fish stress or death

        1. Ensure the water pump, air pumps, and bell siphon are working.

        2. Make sure the temperature is at the ideal level.

        3. Add aeration.


        Temperature is too high (>33°C) or too low (<15°C)


        Fish are not eating

        1. If you live in a hot climate, ensure your fish tanks are shaded, so the water stays cool.

        2. If it's winter, insulate the fish tanks or use heaters and reduce the amount of fish food

        3. Choose fish species that are suited to your climate 

        Dying fish

        1. Too much food, fouled biofilter, high water temperature

        2. Climate

        3. Air pumps not working, too many fish in the tank

        1. Too high ammonia level

        2. pH swings

        3. Swings in water temperature

        4. Too low DO

        1. Maintain water temperature, clean the biofilter and feed less food

        2. For pH swings, use pH up for low pH level and pH down for high pH level

        3. Monitor water temperature and use heaters if the climate is cold

        1. Use backup pumps and lessen fish in the tank


        An aquaponics system can also become a victim of insect or pests attack. Usually, this is not a big problem, but if left uncontrolled, insects and pests can cause damage to plants resulting in plant death and failure of the system. Below are the methods of controlling pests in aquaponics systems. 


        How to Control


        Wrap posts with cotton


        1. Remove physically

        2. Use beneficial insect such as ladybug beetles, hover fly larvae and plants such as garlic, clover, mint

        3. Organic pesticide such as neem oil extract 


        1. Stir plant stems to stir up traps and remove unhatched eggs

        2. Use sticky trap

        Mealy Bugs

        1. If the infestation is light,dabbed insects using a Q-Tip dipped in a rubbing alcohol

        2. Spray with neem oil extract


        Spray with water


        1. Remove physically

        2. Use of exclusion net

        3. Organic spray

        Algae Growth

        Algae can be a problem in aquaponics when they get out of hand. Preventive measures must be taken to prevent it because, if not appropriately managed, algae can affect the nutrition and pH of your system. To fix algae problems, you can use these two methods:

        1. Shading: Shade your fish tank with a dark-colored trap or a piece of plastic to reduce the algae in your system. Algae need light to grow, so by shading them, you are preventing them from growing. Some growers also paint their white tanks or barrel with black paint and then with white color to prevent algae growth inside the plastic.
        2. Mechanical Filtration: This includes filters, screens, vortex and settlement tanks, and other mechanical means of removing algae from the system. 

        Loss of Power

        A power outage can happen everywhere unexpectedly. As long as it doesn't last, it is a minor inconvenience and will probably bring no damage. However, a power outage can be a major problem when it comes to your aquaponics system. 

        To maintain the delicate balance in your aquaponics system, you must keep your aerationfiltration system, and heater working all the time. These devices are powered by electricity to maintain balance for your aquaponics system.

        Your best option during power interruption is to have a powerful generator to run your water and air pump. However, if you want to save on cost, another alternative is a handy battery-operated air pump, extra air stones, airline tubing, and batteries available in aquarium stores.

        If you have an indoor aquaponics system, the most important thing you can do when your grow lights stop working is to get some light during regular light. Plants will start deteriorating quickly when left in the dark for more than 24 hours. However, you can slow the process by providing them with some light, such as periodically flashing a flashlight over the plants for a few minutes every hour.


        Building and maintaining an aquaponics system can sometimes be challenging, as many variables need to be considered. However, do not be discouraged by the problems you will encounter in keeping your system because those problems will give you experiences to learn from.

        Thank you for reading, and if you have anything to add about the most common problems in aquaponics, please share it in the comments section below.

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