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Table 8.4 lists the most common problems when running an aquaponic unit. If anything appears out of the ordinary, immediately check that the water pump and air pumps are functioning. Low DO levels, including accidental leaks, are the number one killer in aquaponic units. As long as the water is flowing, the system is not in an emergency phase and the problem can be addressed systematically and calmly. The first step is always to conduct a full water quality analysis. Understanding the water quality provides feedback essential for determining how to solve any problem.


Electricity/pump and system problems

Pump not working; electricity is off.

  • Reason: No electric power.
  • Problem: DO will decrease.
  • Solution:
    1. If electricity supply is unreliable, a DC backup power system should be installed.
    2. Take water from the sump tank and pour into the fish tank, temporarily replenishing oxygen levels; repeat this process every 1–2 hours until power returns.
    3. Install a 200 litre container above the fish tank that can release a slow stream of water into the fish tank, creating bubbles.

Pump not working; electricity is on.

  • Reason: Pump is either broken, faulty or clogged.
  • Problem: DO will decrease.
  • Solution: Check and clear any obstructions on pre-filter or in pipes. Replace pump immediately, if faulty.

Pool of water underneath system or water unusually low.

  • Reason: Leaks or cracks.
  • Problem: All water will drain out, stressing and eventually killing the fish and plants.
  • Solution: Fix any leaks or holes immediately. Use standpipe to prevent fish tank from losing water. Replenish water.

Water in system and sides of fish tank looks green.

  • Reason: Algal bloom.
  • Problem: DO will decrease.
  • Solution: Shade the system, and physically remove mature blooms of algae.

Water quality problems

Ammonia or nitrite> 1 mg/litre.

  • Reason:

    1. The bacteria are not functioning.
    2. Too many fish for the size of the biofilter.
    3. Accumulated non-living biomass: uneaten food, dead fish, solid wastes.
  • Problem: Fish will be stressed and die.

  • Solution:

    1. Immediately change 1/3–1/2 of system water with new water.
    2. Remove all uneaten food, dead fish or build-up of solid waste in the tank.
    3. Stop feeding until levels decrease.
    4. Make sure pH and temperature are optimum for bacteria.
    5. If nitrite is high, add 1 g of salt for every litre to immediately neutralize the toxic water quality threat. Afterwards, change the entire water volume over a period of 2 weeks.
    6. Recalculate component ratios, biofilter size and feeding regime.

Nitrate levels> 120 mg/litre for a number of weeks.

  • Reason: High feed rate ratio.
  • Problem: No immediate problems, but toxicities may occur if nitrate keeps increasing.
  • Solution: Exchange water and use dumped water to irrigate crops.

Carbonate hardness (KH) is 0 mg/litre.

  • Reason: All of the carbonate is used by the acid created in the aquaponic unit.
  • Problem: The pH of the water will change quickly, stressing the fish and plants.
  • Solution: Add calcium carbonate (limestone gravel or shells) to the unit.

Fish Problems

Fish are piping at water surface.

  • Reason: Oxygen levels are too low.
  • Problem: Fish will be highly stressed and die.
  • Solution:
    1. Make sure electricity is on and pump is fully working.
    2. Make sure the bell siphon and air pumps are functional.
    3. Make sure system tanks are fully covered to reduce temperature.
    4. Add supplemental aeration.

Fish are not eating

  • Reason:

    1. DO is low.
    2. Ammonia and/or nitrite are too high.
    3. pH is too high or too low.
    4. Fish have diseases.
  • Problem: Fish are stressed and will develop disease or die.

  • Solution:

    1. Perform water quality tests for ammonia, pH, nitrite and nitrate.
    2. Identify why fish are stressed (pH increase, ammonia or nitrite increase, oxygen decrease, organic pollution, disease) and fix the problem.

Water temperature is too high (>33 °C) or too low (<15 °C).Fish are not eating

  • Reason: Climate.
  • Problem: If temperature is too high: fish will stop eating and plants will begin to wilt and die.If temperature is too low: bacteria will stop working, some fish may not eat.
  • Solution:
    1. In summer, make sure system tanks are shaded so the water stays relatively cool.
    2. In winter, first isolate and then insulate the fish tanks. Then, use solar or electric heaters, and reduce the amount of fish food and vegetables growing in the unit.
    3. Change fish species with ones more appropriate for that climate.

Plant Problems

Plants are not growing and/or leaves are changing colour.

  • Reason: Plants are deficient in some essential nutrients (or temperature is too high for certain plants, plants are diseased).
  • Problem: Plants will not grow or produce fruit.
  • Solution:
    1. Make sure water quality is optimum for plants.
    2. Check nitrate levels: if they are too low, slowly increase fish feed per day.
    3. Check if there is any root/stem disease.
    4. Add aquaponic-safe fertilizer to plants.

Nitrate levels are high yet plants leaves are yellowing

  • Reason:

    1. pH is not at optimal level (too high or low).
    2. Plants are deficient in some essential nutrients.
  • Problem: Plants will not grow fully or produce fruit.

  • Solution:

    1. Check if the yellowing is on new or old leaves. If on new, add iron up to 3 mg/ litre.
    2. Check pH and adjust if it is not optimum.
    3. Add aquaponic-safe fertilizer such as compost or seaweed tea to plants.

Vegetables surrounding the water entry pipe are thriving while other vegetables farther away are struggling.

  • Reason: Vegetables around the entry pipe are taking up all the nutrients.
  • Problem: Uneven growth of vegetables in media beds.
  • Solution:
    1. Spread the water all around the grow beds using irrigation pipe with small holes.
    2. Remove the media bed standpipe every day to flush the water in the media bed out into the sump tank.
    3. Check nitrate levels; if too low, slowly increase fish feed given per day.

Source: Food and Agriculture Organization of the United Nations, 2014, Christopher Somerville, Moti Cohen, Edoardo Pantanella, Austin Stankus and Alessandro Lovatelli, Small-scale aquaponic food production, Reproduced with permission.

Food and Agriculture Organization of the United Nations

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