Nutrients and Bacteria in Aquaponics

Plants Growing in aquaponics system

Nutrients are one of the most exciting and yet still mysterious aspects of aquaponics. For fish, this is mainly related to food, which the grower provides. For plants, the nutrients primarily come from the food provided to the fish. However, some amendments such as iron, calcium, and potassium may be needed as these nutrients not usually found in fish food. 


Fish produce ammonia, most of which enters into the water through the fish gills. A small portion (approximately 30%) of the ammonia enters into the water through the solid waste excreted by the fish. In addition to the waste from the fish, as much as 25% of the feed given to the fish remains uneaten, producing additional solid waste.

These solids need to be removed from your aquaponics system. When left in the system, they can harbor harmful bacteria, the way uneaten food in a refrigerator can eventually start harboring bacteria and fungus.

Research at the University of the Virgin Islands (UVI) established that it takes 60-100 grams (2-3 ounces) of fish feed each day to provide sufficient nutrients for every square meter (9-10 square feet) of grow bed area. The UVI system includes three stages of filtration to pull the solids out of the water coming from the fish tank before the water reaches the plant grow beds. The first stage pulls out most of the large solids. A second stage allows fine solids to collect on mesh. The third stage introduces oxygen to optimize water quality before the water enters the grow beds. The solids from these filters are emptied every day and put into an aerated “lagoon” and provided to local farmers as fertilizer.

Other farmers will take the solids and put them into aerated biodigesters, allowing the nutrients to become water soluble. The nutrient-rich water from the biodigesters is returned to the aquaponics system. This can increase the amount of growing area supported by 60-100 grams per day from ~10 square feet to 20-30 square feet.

Some farmers wish to ensure their plants have enough nutrition, and will add some hydroponic nutrients to their aquaponics system. But this isn’t always beneficial. Excessive nutrients actually can inhibit the microbial activity necessary for optimal plant growth.

Three of the nutrients typically added to an aquaponics system in addition to fish feed are:

  • Iron - To produce chlorophyll. Yellowing leaves is one sign of possible iron deficiency. Fish usually lacks sufficient iron. Your best option is chelated iron which is designed for use in aquaponics systems. Avoid standard iron that you might buy in a garden center which often contains a significant amount of lead.
  • Calcium - to support the transition from blossom to fruit. Calcium powders also helps buffer the water to maintain pH in a stable range. Too much calcium, however, will raise pH to a range that locks out nutrient uptake.
  • Potassium - promotes healthy fruit production. Potassium powders, like calcium powders, help buffer water.

In the UVI research system, iron, calcium, and potassium are added on a daily basis. The amount required and how often you might need to add these nutrients will depend on what you are growing and the size of your system.



There are two types of bacteria in aquaponics systems: beneficial bacteria and bad bacteria called pathogens. Beneficial bacteria is actually required in order to run a successful aquaponics system.

Bacteria and Pathogens in Aquaponics

Beneficial Bacteria

Beneficial bacteria transform animal waste into plant nutrients. Beneficial bacteria is the engine that makes aquaponics work.

Fish produce ammonia as a by-product of living. The majority of this ammonia goes directly into the water through the fishes’ gills. The simple presence of this ammonia attracts the nitrifying bacteria that like to “eat” ammonia and eventually transform it into the nitrate plants need.

A mature aquaponics system is a richly biotic environment, producing lush growth. But a new system may need to cycle for weeks before the nitrifying bacteria are robust.


Pathogenic Bacteria

Fish rarely harbor human pathogens, however, aquaponics is not immune to food-borne illness. Backyard gardens and small farms do not typically produce enough food to require regular testing for pathogens.

Best practices to avoid pathogens are:

  • Grow your aquaponics system in an enclosed greenhouse.
  • Keep household pets and animals other than fish away from your system.
  • Learn how to keep healthy fish and follow these measures.
  • Wash food before eating(1). 



Understanding how the nutrients and bacteria play a role in your aquaponics system is an important step in understanding how aquaponics works. The next article will discuss the construction and building of an aquaponics system. Join our newsletter below to be notified when our new articles are posted!




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