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8 Most Common Problems in Aquaponics: Why it Fails & Fishes Die

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Every aquaponic system faces problems that are not uncommon. By being aware and understanding the problems aquaponics systems are faced with, you can have an advantage in addressing them before they arise.

The most common aquaponic problems are:

  1. Plant deficiencies
  2. Lack of Proper Aeration
  3. Dying Plants and fishes
  4. Pests
  5. Algae growth?
  6. pH swings
  7. Water Temperature?
  8. Loss of Power

See our complete guide on aquaponics and what you need to know to run a successful system.

My Aquaponic setup

Build a successful system with these affordable equipment from amazon, that I’ve tried & tested on my setup.

Click on the links to see them

Best water pump
Best Water Pump
Best air pump
Best Air Pump
Best air stone
Best Air Stones
GROWNEER 25 Packs 4 Inch Garden Slotted netcups
Plant Net cups
Bio Balls
Bio Filter Medium
API Freshwater Master Test KIT 800-Test
Water Test Kit
The Aquaponic Equipment Essentials that I use in my system.

1. Plant deficiencies – 

Plants in the aquaponics system can have the same deficiencies as normal plants. After all, they are plants, and the only difference is that they are grown mainly in water.?

Aquaponic plants require a ratio of Nitrogen to Phosphorus to Potassium (N:P:K) and other trace nutrients such as boron, copper, chloride, zinc, magnesium, calcium, iron, and manganese. All these nutrients play an integral part in proper plant growth.

Luckily most trace nutrients are provided by the food which are being fed to the fishes. So take a look at the ingredients in your fish food and you will have an idea of what is also being provided for the plants.

Nitrogen deficiency

Symptoms include poor plant growth, and leaves become pale green or yellow because they are unable to make sufficient chlorophyll.

This can be easily corrected by adding more fish to the system.

Potassium deficiency

symptoms in plants include brown scorching and curling of leaf tips as well as chlorosis (yellowing) between leaf veins.

Potassium can be added to aquaponics systems by either directly spraying potassium onto the leaves of the plant which has to be done periodically.

Another way to add potassium to the system is by adding over-ripened or dark to black banana peels directly into the biofilter. Kelp meal concentrate also does a good job. This would create a slow release of potassium into the system and would prevent shocking the plants.

Phosphorus deficiency

Plants will show stunted growth, darkening of the leaves near the base of the plant, and a purple or reddish color.

Phosphorus can be added to the system by using chlorine-free super triple phosphate or rock phosphate in a quantity of 20 to 40 ppm or parts per million in your system for fruiting plants.

I have made a table that would make it easy to identify the deficiencies and how to correct them.

NitrogenStunted Growth, Pale color, Light green yellowish leavesAdd more fishes to the system
PhosphorousStunted growth, darkening of the leavesAdd super triple phosphate or rock phosphate
PotassiumBrown scorching and curling of leaf tipsadd Kelp meal or old banana peels to biofilter
MagnesiumPaleness from leaf edges. Edges have cup shapes foldsUse leaf spray, such as Epsom salts
IronLeaves are pale, No spots, major veins GreenAdd Fe-DTPA soluble chelated Iron
CalciumPlant dark green, Drying starts from the tips, Tender leaves paleSpray calcium chloride onto leaves
Borondiscoloration of leaf buds. breaking and dropping of budsfound in trace amounts in fish food
CopperPale pink between the veins. wilt and Drop.found in trace amounts in fish food
ZincLeaves pale, dark spots on leaf edgesfound in trace amounts in fish food
Molybdenumspots on whole leaf except veins. Leaves light green or yellowfound in trace amounts in fish food
SulphurLeaves light green, veins pale greenfound in trace amounts in fish food
ManganeseLeaves pale in color, veins dark greenfound in trace amounts in fish
Plant Deficiency and Correction Table

2. Lack of Proper Aeration

The process of respiration occurs continuously in an aquaponics system, and organisms from the fishes to bacteria, all need air to survive.

The air the fishes and plants in an aquaponic system use is in the form of dissolved oxygen. Dissolved oxygen enters the water through turbulence created by the air pump with stones and the bubbles they produce.

What can cause the Dissolved Oxygen in the Water to Drop?

The dissolved oxygen in an aquaponic system can fall because of a number of reasons.

  • Algae starts to invade the Aquaponics system
  • The air pump stops for some reason
  • The air stones are fouled.
  • The temperature of the water increases
  • As the biomass of the fishes increases
  • There is additional plants in the system
  • There is other organisms in the system eg. snails

3. Dying Fishes – 

Fishes in aquaponics can die from a lot of different causes. Major changes in the environment can have an adverse effect on the fishes causing them to be stressed and eventually die.

Continuous water quality monitoring will prevent fishes from dying if you can correct the problem quickly. 

The reasons fish die

Ammonia Levels HighToo much Food, Fouled Biofilter, High water temperatureMaintain Water temperature and clean biofilter, feed less food
pH swingsFouled biofilter, High Water temperatureUse pH Up for Low pH and pH down for high pH
Swings in Water TemperatureWeather conditions, ClimateMonitor water temperature and use heaters to maintain
Lack of Dissolved OxygenAir pump shuts down, Water temperature too high, Too much fishesUse backup air pump, Reduce fish count, control water temperature

4. Pests – 

There many types of pest which can affect plants in aquaponics systems. It usually starts with a subtle introduction and before you know it, the entire crop can be totally wiped out.

For this reason it is important to have some type of defense in the event of a pest attack. Other preventative methods can also be used to help prevent pests and insects from invading and destroying your entire aquaponics system

In aquaponics, the best method of pest control is always using an organic approach. Meaning using pesticides derived organically from plants which will repel and remove any unwanted pests.

These pesticides should not contain any man made chemicals or additives which may end up in the plants and eventually in our plates.

AntsWrap Posts with Cotton
AphidsUse ladybugs or Neem Oil Extract
CaterpillarsRemove by hand
MealybugsSpray with neem Oil Extract
CutwormsSpray with neem Oil Extract
FrogsUse Barrier Nets
Iguanas (yes Iguanas!)Remove by hand, use Barrier nets
Pest control Table

5. Algae growth –

Algae can be very sneaky. First, it starts small and you don?t think much of it then after a few days the entire system is covered with it. Algae may seem like a minute problem but left unchecked can destroy any aquaponic system, fast!

Aquaponic systems are rich in nitrates, a form of nitrogen nutrient that green leafy plants love. Algae are green in nature and are made up mainly of chlorophyll which uses nitrates to give the bright green color we know it to be.?

Hence the reason to ensure they should be kept at bay in aquaponics.

If not, they can grow wild and foul the entire system, consuming nutrients and dissolved oxygen which will eventually starve both plants and fishes leading to their deaths.

6. pH Swings –

Aquaponics systems work best in pH ranges between 6.8 to 7.0?

Fishes and bacteria prefer a pH range between 7.0 and 8.0 and plants prefer a pH range between 5.5 to 6.5.

pH swings can occur mainly because of the chemical balance in the aquaponic system. Higher concentrations of ammonia can cause pH levels to be elevated which may well exceed the 8.0 pH range.

This will cause fishes and plants to die rapidly since ammonia is toxic to both of them.

On the other hand, the pH can also go in the other direction as the nitrification process occurs, meaning that it can drop below the 6.0 pH level.

Although some plants love this and may not be affected by it, the water becomes too acidic causing a very stressful environment to the fishes which may eventually die if the pH is not corrected soon.

7. Water Temperature – 

The temperature of the water plays a very important role in how well an aquaponic system performs. The temperature of the water can affect both fish and plants.

The ideal temperature for aquaponics should be held between 18?30 ?C or (65F – 86F) since within this range it favors fish, plants, and bacteria growth.

High water temperatures will affect the rate at which oxygen is dissolved into the water stream. Less oxygen will get dissolved into the water causing the dissolved oxygen levels to drop.

This can result in both fishes and plants dying due to insufficient oxygen.

Bacteria thrive in warm temperatures and produce the best results at temperatures between  77-86 F (25-30 C). Temperatures below this can cause bacteria activity to fall.

This in turn will cause the conversion of ammonia to nitrates to also drop. The result will be fewer nutrients for plants and also higher ammonia concentrations.

8. Loss of Power – 

The reliability of power in your area will play a role in how well your system performs. With a loss of power, the entire aquaponic system shuts down.

The air pump stops meaning that the dissolved oxygen in the water will be diminishing as time passes. The fish will eventually die from a lack of oxygen.?

The pump on the other hand also stops causing the entire system to come to a halt. There is no more water circulation and the rich supply of nutrients that the plants enjoy will be cut.

This will not adversely affect both plants and fishes in the first couple of hours since the plants will have some residual nutrients and the water in the fish tank will remain there.

After some time both fish and plants may die if nothing is done.
A simple solution to this is to install a backup power system that would not interrupt the power supply in the event of a power failure.?

This can take the form of a DC air and water pump or a battery bank with an inverter that switches on when there is a power loss from the mainline. This is a simple addition that is crucial to the success of an aquaponic system, especially if the power grid is not reliable.

Not So Common but it Happens…

The Picture at the top of this post was taken a year ago. I had 30 koi and they were all growing very healthy. I checked and fed them routinely until one morning I discovered that all the fishes were dead.

It was a frog, A FROG! He decided to leap into my biofilter. He couldn’t escape so he released stress chemicals from the pores of his skin into the water.

Apparently it’s poison to the fishes and kill every last one. My entire system failed and I had to shut down and restart the system from scratch again.

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