The Most Common Aquaponics Problems - Go Green Aquaponics

The Most Common Aquaponics Problems

Problems are unavoidable in every aquaponics system, and failure to solve these problems could cause losing the plants and fish that you've nurtured for weeks. This could also leave a disappointing feeling of losing the time, efforts and money spent in setting up an aquaponics system. That is why it is important to know the most common aquaponics problems and how to deal with it.

Depending on the problems that an aquaponic farmer may encounter, surely there are different solutions available. Some problems may be quite simple to fix, while some may be more complex. Let's dive in and discuss these problems that others have faced in their aquaponics system.

Raft Aquaponics System

1. Plants Are Dying

There can be many reasons the plants in your aquaponics system are dying, which include:

  • Insufficient water and oxygen:What you need to do is make sure that your plants are getting plenty of water and oxygen. To do this, you need to check the roots to see if they are healthy. 
  • pH levels: Plants, fish, and bacteria are the three major elements that must be considered in checking your system's pH level. Each one of these elements prefers a slightly different range of pH, so it is important to keep your system in the ideal pH range. Fish and bacteria prefer a slightly alkaline environment, while plants prefer a more acidic environment. So, the ideal range for most aquaponics systems is a pH of 6.5 to 7.0.
  • Bugs/Pests:Bugs can harm or kill your plants, so check your plants leaves for any signs of pests. 
  • Iron Levels: You also need to check if your water has enough minerals, especially iron. You can supplement your aquaponics system with chelated keep your plant healthy.

 2. Too Many Fish in the Tank

Too many fish will overcrowd your fish tank and make your system less efficient. It is advisable not to fill your fish tank and keep stocking density low if you are starting your system. With low stocking density, you can easily manage your aquaponics system and avoid any shock and collapse. 

Too many fish will release lots of fish wastes that will be more than what the plants can filter. A good rule of thumb is to keep one fish per every eight gallons of water. Anyway, you always have the option to add fish later when you see that your system needs more fish. So, it's a waste to overstock fish and lose them to death or have to take them out.

Fish in the Fish Tank

3. Pest Problems

Just like any farming method, pests can also be a problem in aquaponics, and it is important to consider the use of natural pest control for establishing and maintaining your system. Keeping your aquaponics system is one way to make sure that the plants and fish in your system are safe and edible.

The most common pests in aquaponics are:

  • Aphids
  • Caterpillars
  • Tomato Hornworms
  • Bettles
  • Mealybugs
  • Cutworms

There are several ways that you can safely eliminate pests from your aquaponics system without using chemicals, and here are some of them:

1. Check your plants regularly for pests.
2. Hand remove visible pests that you find in your plants and destroy the pests.
3. You can use bug netting in your aquaponics system to create a physical barrier around the plants to prevent many pests from getting to your plants.
4. You can plant pest-repelling plants in your system to drive away from the pests. You can plant these plants beside your vegetables. Pest-repelling plants are artemisia, catnip, dill, chives, chrysanthemums, petunias, and mint.
5. Use beneficial insects such as ladybugs, lacewings, and spiders. These are beneficial insects that can help in preventing or controlling pests in your plants.

4. 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 managed properly, algae can affect the nutrition and pH of your system.

The most common algae that causes problems in aquaponics are the green algae. Algae can cloud up the water in your aquaponics system, foul pipes, and pumps and can cause oxygen depletion and pH swings.

To prevent algae from growing in your system, you have to make sure that the temperature of your aquaponics system is appropriate for the plants and fish and make sure that the phosphorus level is not too high.

To fix algae problems in aquaponics, the two easiest methods are by shading and mechanical filtration.

  • 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 Aquaponic farmers also paint their white tanks or barrel with black paint and then with white color to prevent algae growth inside the plastic.
  • Mechanical Filtration: This includes using filters, screens, vortex and settlement tanks, and other mechanical means of removing algae from the system. 

5. Dead Fish

Dead fish happen in an aquaponics system sometimes, but if there's over one dead fish in your system, you need to check your system. The first you need to check is the ammonia level. Too much ammonia can kill your fish, so you need to check your ammonia levels regularly. However, if the problem continues, you need to check all of your system's components to make sure that there is plenty of oxygen in your water. 

6. Water Temperature

Different fish thrive in different temperatures, so it is important to choose fish species that will thrive in your location and climate. Another important thing to consider also is selecting the location for your fish tank.

If you have an outdoor aquaponics system, make sure that your fish tank is not exposed to the sun for most of the day. Too much sun can make your water warmer, that can decrease the oxygen level in your water that can harm the fish. There are several tips in monitoring the water qualityof your aquaponics system and knowing these will be a big help in maintaining your system. 

7. Contaminated Water

Using water that may not be clean is a big risk in aquaponics. So be sure to use clean water in your system like rainwater and potable pH neutral well water. If your water is treated with chlorine, it must be removed before it can be used in the system. You can remove the chlorine by allowing the water to be used to sit out for 24-48 hours before using it. Chlorine gas will dissipate during the resting time, leaving a clean and dechlorinated water. 

Nutrient Deficient Tomato Leaves in Aquaponics

8. Plant Nutrient Deficiency

Plant nutrient deficiencyin your aquaponics system can affect plant growth and ruin your harvest. Plant deficiencies happen when various nutrients are not readily available in the water or fish wastes that are used to feed the plants.

 Recognizing your problem and identifying what your plant's nutrient needs are important in preventing and treating plant nutrient deficiency problems in your system.

The most common plant nutrient deficiency in aquaponics systems are:

1. Potassium Deficiency: Potassium is essential for healthy root development, seed, and fruit growth. Plants with potassium deficiency have a browning or burnt look on the leaf tips, curling of leaf tips, yellowing of the leaf veins and purple spots on the underside of the leaves.

Severe potassium deficiency can lead to plants. You can supplement potassium to your system by applying it foliarly (spraying it on the plants leaves) using potassium chloride or by adding potassium solution to your system by using potassium hydroxide, kelp meal concentrate or potassium sulfate.

2. Iron Deficiency:Iron is used to produce chlorophyll with other enzyme production functions. Signs of iron deficiency in aquaponics plants are yellowing of leaves in between green veins, a web-like pattern on the leaves, and stunted plant and leaf growth.

Iron deficiency in plants needs to be treated because it could cause the failure of new plant growth, the inability of plants to blossom or produce fruit and can cause plant death. You can supplement iron in your system by using chelated iron.

3. Calcium: Calcium is important for plant growth, the strong cell wall of the plants, production of flowers and fruits, and helps plants maintain their strength and shape. Squash, tomatoes, and peppers are most susceptible to calcium deficiency. Death of young leaves, flowers and fruits, blossom end rot, and deformed new growth of leaves are the common signs of calcium deficiency.

Calcium deficiency in your aquaponics system requires swift action because this can ruin your harvest or cause plant death. You can treat calcium deficiency in your system by using a supplement or by foliarly applying calcium chloride to your system.


Building and maintaining an aquaponics system can be challenging at times, as many variables need to be considered. However, once you have established a system on maintaining your aquaponics system, everything will be easy. Do not be discouraged by the problems that 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.

1 Response



May 31, 2022

What is causing silvery spots on my swiss chard? Sometimes the one next to it is fine. It happens on mature plant and then they die.

Leave a comment (all fields required)

Comments will be approved before showing up.