Aquaponic Nutrients: What happens to them in your aquaponic system?

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Aquaponic Nutrient Fates and Some Brief Terminology

Before we really dig into nutrients, we have to understand what happens to them in the system. 


How Do Nutrients Enter the System? *

Almost all of our nutrients enter as organic solids- that is, nutrients tied to organic molecules (carbon chains!).


These organic molecules are broken down in the system, by the fish, microbes, other organisms and chemically.  As they are broken down, the nutrients usually become an inorganic ion on solution.  This means that they become a charged molecule/ion that is dissolved in the solution, making them available to the plants.


How Do Nutrients Leave The System? *


Now we know how nutrients enter the system, but most folks don’t think of the ways that they leave the system.  Nutrients available to our plants are lost a number of different ways, including:

Removal from the system in the form of plants or fish, losses or waste

In this scenario, the nutrients are lost- often completely.  Once that fish is harvested, you never get it back, and unless you’re composting leftovers from your plant harvests, those nutrients are gone too.  This is totally fine- it’s the way it’s supposed to work.  In some systems solids are actively removed- this is good for certain production systems but can sometimes represent a significant amount of nutrition leaving the system.


Sometimes however, nutrients are lost when water from the system leaks out or when other disasters strike- these types of losses are bad for many reasons, and can represent serious headaches for aquaponics practitioners.


On the flip side of this too, is when nutrients unexpectedly enter the system in force- one instance of this is a dead fish.  In this instance, nutrients tied up in the fish, and expected to leave the system, are suddenly released into the solution, causing problems of their own.


Aquaponic nutrients become tied up

Oftentimes, nutrients are put into a system but don’t reach the plants (at least for a while) because they are captured and tied up by other organisms.  This is common in all systems but especially apparent in beginning systems with algae blooms.


In these systems, as the user adds nutrients, they disappear almost immediately, and often their plants show deficiencies.  This is because the algae is tying up the nutrients before the plants have a chance to get them, resulting in all of the nutrients being tied up in algae biomass, while the plants starve.  Eventually, the system will reach equilibrium.


At this point, algae is dying and releasing nutrients back into the system at the same rate as it is taking it up.   In this phase, dying algae can represent a great reserve of stored nutrients- which depending on the growing technique you are using can represent an asset or a problem.  Solids tolerant systems can use these nutrients, as they allow decomposition cycles to take place within the system.  Raft and NFT systems must remove the algae so as not to foul plant roots and consume oxygen as the algae dies and decomposes.  In this way, these systems avoid this nutrient-sink problem altogether, but it does represent serious additional costs!


There are many other organisms that participate as nutrient sinks in systems, and the growers who implement the most complex systems just get used to the more complex and time consuming cycling.  Typically, while some nutrients are lost in this process (just due to the inefficiencies in the various cycles), nutrients tied up in algae, worms or bacteria are only temporarily lost.  Eventually, as the system establishes, all of these tied up nutrients begin to become available and in the long term serve as a sort of “bank” for your system.


Aquaponic nutrients

Dr. Nate Storey discussing aquaponic nutrient fate and terminology.

Nutrients in the system but not available- i.e. precipitates


Precipitates are tricky things.  Most mineral nutrients will form precipitates of one form or another if given the correct set of circumstances.  pH and oxygen play the largest roles in these transformations from usable, helpful elements to worthless, unusable solids.  Fortunately for us, for many compounds the conditions required to form precipitates are either relatively extreme, or simply aren’t that common in aquaponic systems.


Precipitation is when a soluble form of a mineral nutrient combines with another element or compound to become an insoluble solid.  This is a very frustrating process for practitioners to experience, and is best illustrated by iron.


Iron loves to form precipitates in aerobic conditions.  It joins with all sorts of other elements to become a solid, and once it does, the plants can no longer access it (except through chelation!).  Many other nutrients do the same thing, and even though they are entering the system, they are not available to the plants.  In some instances (and we will talk about this wit potassium) precipitation is caused by an increase in another element in solution.   While in others precipitation reactions govern or are governed by pH (as is the case with carbonates- a group of substances that can cause beginning systems a great many problems).  All of these will be addressed in this series.


Stay Tuned *


This is the beginning, and I am glad that I have the chance to (however briefly) address nutrient fate, and some of the jargon that will have to be used to thoroughly explain how many nutrients act in these systems.

If you failed your high school chemistry class, do not fear, as we begin to explore these elements I will do my best to explain what they are doing simply, and make the subject as clear an interesting as it truly is.




  1. Good stuff Nate, looking forward to details! Great introductory material. Working on design and hoping to break ground on my system ASAP!

  2. great info. thanks so much

  3. Love your work Nate, intrigued to find out about carbonates, my FT is an old plastered concrete pool and I struggle to keep the pH below 8. my system is over 6 months old but plant growth is almost non existent. it’s painful to see others bragging about massive plant growth after just weeks.

    • Hello Steve, when I think of plaster I think of lime (mortar).
      Is it possible to take a sample of the plaster surface of your pool? You can do a simple test with the growing medium but I think the test is valid for the container(s) you are growing in.
      The test consists of a sample of medium and/or surface material of either fishtank or growing containers put in a glass. Add some ordinairy vinegar and observe the surface of the sample pieces. If bubbles occur, you know the material isn’t acidity resistant and most likely also not alkaline resistant and thus unsuited for Aquaponic application.

      • Thanks, You are right the concrete pool is finished with a lime type hard plaster. And when I did the test yes it bubbled, guess my system is screwed now. Looks like I am up for a total redesign of my system unless there is a way to negate the affect of the plaster.

        • Hi Steve, I guess a chemical solution/countermeasure (=shortcut) is thinkable but in essence impractical because you would need lots of the countermeasure chemical.

          I am sorry to say but you need to find a way to put in some sort of a plastic HDPE or alike liner in to prevent water from “nibbling” at the paster.

          After that you should have a good system…
          Also I would redo the match.. It is widely excepted that 1 volume of fish tank should be balanced by 4 volumes of grow bed/biofilter media. This is when the depth of the grow bed is about 9 inches.
          Ussually swimming pool based fishtanks (unless left very shallow) tend to be grossly out of this 1 to 4 balance…resulting in too much nutrients which is possibly as bad as too little nutrients…

          If I had a swimming pool in my yard I would attempt a natural pond combined with aquaponic grow beds for both filtration and growing crops…
          In your case the lime paster is a bump in the road but in case of a natural pond relatively easy solved by putting in a (welded) HDPE liner

          Best regards, Sander Tel.

        • Sander Tel is on the right track, look into an HPDM liner- you could put it in the system seal everything and get it running again in no time!

          • I would love to see some pictures (or even a video) of the current situation.
            Would be good to see the pool step into the lime (ahum) light…
            Regards, Sander.
            PS: maybe it is possible to used the pool as a “room”and set up several IBC totes to house: fish: DWC and other growbeds. HDPM plastic sheeting can be a big hassle installing, especially in large areas…

          • Thanks Nate, appreciate your help. I have purchased a LDPE liner which should be installed soon. I am interested in how carbonates affect the aquaponics system nutrients?

            As aside I added 50ml of H2SO4 (to 8kl FT) 25 days ago since then the pH seems more stable albeit at 7.4 – 7.6 and the plants seem to have picked up a bit. previously I was trying to control rapidly rising pH with HCL (75 – 100ml per week) to no avail!
            I used H2SO4 as I saw in relation to plant irrigation our Ag dept recommending pH lowering via H2SO4 as it would enable plants to better access nutrients, is this also true in aquaponics systems?

            Also during the last few weeks, the temperature has risen fish are feeding more, plus the fish have multiplied, the Nitrates are over 80 now.

            Looking forward to the liner install and getting the system working properly.

            regards Steve

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