Optimising An Aquaponics System – Part 1

Aquaponics is demonstrably a great way to produce clean fresh food.

Like any good idea, however, aquaponics has attracted its fair share of opportunists and false prophets.  Simplistic guidelines and exaggerated performance claims have resulted in many system failures.

The fact is that keeping fish is the same as keeping any other type of livestock – it comes with responsibilities.

They need to be stocked at appropriate levels, fed properly and provided with appropriate accommodation.  They need to be checked at regular intervals and their quarters kept clean.

Failure to undertake these responsibilities around any livestock will (at best) result in lost productivity and (at worst) in diseased or dead stock.

For most of the past four years, we’ve run several small aquaponics systems simultaneously.  We’ve trialled different configurations, species and age groups.

Our experience confirms the following:

  • It is not useful to make generalised stipulations around stocking rates because of the variables involved.
  • With smaller systems, things happen faster…..for better or for worse.
  • An aquaponics system that is equipped with effective mechanical and biological filtration will produce more fish in greater safety than any basic fish tank/grow bed model of an equivalent size.
  • The only sure way to be certain that a system is in good health is to test the water – and manage the unit according to the results – on a daily basis.

At the popularly touted 2:1 (grow bed volume to fish tank volume) ratio, it is unlikely that even the frequently recommended 20 – 30kg (per 1,000 litres) stocking density, may be sustainable for some species.

Remember, these stocking densities were originally premised upon tilapia – a very tough species known for their ability to survive in water of indifferent quality.

For some species, the stocking density is much less….something in the order of 5 – 10kg per 1000 litres of water.

When I first suggested that simplistic guidelines and exaggerated stocking rates were largely responsible for the daily procession of fishkill stories on aquaponics forums, I was greeted with howls of protest.

Over time, however, we demonstrated that the ‘one size fits all’ approach to aquaponics wasn’t going to work for many people and a new rationalisation began to emerge.

Some of our critics began to recall how their systems functioned best when very lightly stocked.   To support their contention about low stocking densities, they began to speak about how, since aquaponics was really more about plants than fish anyway, low stocking rates were really the way to go.

While it was useful that these people began to acknowledge that the standard aquaponics system had stocking limitations, this position ignored the fact that it cost the same amount of money (in terms of component costs) to house ten fish in 1,000 litres of water as it does to house 50.

It also costs the same amount of money to pump water for 10 fish in a tank as it does for 50 fish in a similar quantity of water.

Fish production is not the only issue. Fifty fish will support many more plants than ten fish.

What these folks failed to grasp was that throttling the system was not the only option.  What we (and others) proved is that, through changes to system design and operation, you can improve the productivity and resilience of the standard flood and drain aquaponics system.

If you are going to maximise the return on your investment in system components, energy and time, you need to grow the maximum weight of fish and plants in the shortest possible amount of time.

The alternative is to waste money, energy and time.

The good news is that you can enhance your existing aquaponics system (without spending a cent) by:

  • Ignoring simplistic guidelines – they’ve got us to where we are now – a mounting tally of dead fish stories.
  • Matching the stocking density to the nitrification and aeration capabilities of the system…and the only way that you can do that is through….
  • Testing water quality…..very regularly!  Forget the nonsense about “sniffing the water” (a recommended alternative to testing from one “guru”) – you can’t detect low oxygen levels (the principal cause of fish deaths) by nose.
  • Manage your system according to your water quality test results……and take appropriate action…..immediately!   Don’t wait until tomorrow to address low oxygen or rising ammonia/nitrite levels – you’ll only need a convergence of other things like hot weather, an algae bloom or overfeeding…….to push abnormal levels to fatal ones.

Anecdotal evidence from many other people supported our own observations that the most productive aquaponics units were those that were subject to rigorous testing and maintenance routines.

In the best managed systems, things can still go wrong and it’s how you handle those situations that will largely determine whether you’ll get to cook and eat your fish or cry over them at their wake.

When your test results evidence a current or looming water quality issue:

  • Stop feeding
  • Check your tank bottom for uneaten food and remove it.
  • Increase the flow rate through your system – more water flow means more nitrification and aeration.
  • Add salt – at the rate of 1 – 2 parts per thousand.  That’s 1 – 2kg of salt to each 1,000 litres of water.
  • Boost aeration – there are very few water quality issues that will not benefit from more oxygen.
  • Change water – if things are not moving quickly in a positive direction.  This might be seen in some quarters as wasting water (that depends entirely on what you do with it next) but having your fish die for the want of a water change is just plain dumb.  Limit your water change to that needed to address the problem.

These things amount to a rite of passage rather than a real passport to productivity – they’re things that you must do just to stay in the game – and they apply to any aquaponics system.

Other useful ideas include:

  • Placing an orphan sock over the inflow pipe and  rest this on a piece of filter foam  This will trap much of the sedimentary solids and some of the suspended solids…..and takes just a few seconds each day to rinse out.
  • Placing a handful of composting worms in the system bio-filter. They will not only assist the mineralisation of those solids that do make it into your grow beds but they’ll also reduce their volume.
  • Set your grow beds up so that they can be cleaned easily.  We use clay pebbles in our beds and, where practical, we limit their depth to 150mm.  This makes cleaning our grow beds as easy as dragging our hands through the media to trap the roots from recently harvested plants.  We periodically flood the beds up and stir up the media while draining the watery solids onto our soil-based gardens.
  • If your fish tank is such that uneaten food or solid waste accumulates on the tank bottom, remove it on a daily basis…..before it begins to putrefy and generate ammonia.

These few simple strategies will extend the productivity and resilience of your aquaponics system…..and they’ll cost you nothing but a bit of time.

To summarise, keeping any form of livestock comes with daily responsibilities and fish are no different.  Spending a few minutes each day on water testing and making appropriate adjustments to your system will allow you to optimise the return on your investment of time, energy, money and effort.

While this may be a disappointment if you purchased your system on the premise that all you had to do was add water and fish, reconcile yourself to the fact that empathising with other aquaponicists about fish kills is much easier than standing in their midst.

In my next post, we’ll show you how to re-configure your aquaponics system for even greater productivity and resilience.



  1. Paul V says

    Well said.

    I would go easy on the salt addition, especially if you do not know how much salt is in the system before you treat it (EC/TDS meter anyone?). Sure it provides benefit to the fish but in a well stocked and managed system, you will not really need it as a prolonged exposure. If you do it is best to treat the fish outside the system at a higher dose.

    Remember sodium chloride is not taken up by plants to any degree, especially sodium (chloride in small amounts) and therefore accumulate. It is diluted when you top up your system with new water but generally, you will be exchanging, on average 5% of your water per week, which means it can take up to 20 weeks (5 months or longer in winter) to completely dilute the salt.

    Sometimes in the back yard, having more tanks for treatment is not often the case, though it is a good idea. Also handing fish is not much fun for both the human and the fish, so permit me to provide you with a solution:
    Lower the water level in your fish tank to half
    Store that water elsewhere for reuse.
    Increase the aeration with adequate air stones.
    Treat the fish at the required salt level for the issue you are having (usually no more than an hour).
    Then fill the fish tank back up again to dilute the salt by 50%. Fish treated, salt use reduced, fish not handled, no spikes in your hands, everyone happy. Important to note, Aquarium stones are not adequate and if you do not have an air pump, I strongly suggest you invest in one sized for your set up. As the salinity of the water increases, the oxygen saturation of the water lowers so air is really needed.

    I might add that any changes or disturbances, cleaning etc.. are best done when the temps are low, like now in AU. It is good practice to make any big changes to your system when everything is happening a great deal slower (when it is cold). This will get everything sorted, clean and ready for the next growing season. Keep in mind that for every 5C temperature increase, everything (nitrification, respiration, pooing, metabolism, feeding) increases by around 50%. So while all the organisms in your eco-system are having a rest, it is a great time to get everything nice and ready for the next growth season. Trying to clean your grow bed in summer may have a negative effect on everything else living in the water with it.


  2. says

    Sometimes in the back yard, having more tanks for treatment is not often the case, though it is a good idea. Also handing fish is not much fun for both the human and the fish, so permit me to provide you with a solution:Lower the water level in your fish tank to halfStore that water elsewhere for reuse.Increase the aeration with adequate air stones.Treat the fish at the required salt level for the issue you are having (usually no more than an hour).Then fill the fish tank back up again to dilute the salt by 50%. Fish treated, salt use reduced, fish not handled, no spikes in your hands, everyone happy. Important to note, Aquarium stones are not adequate and if you do not have an air pump, I strongly suggest you invest in one sized for your set up. As the salinity of the water increases, the oxygen saturation of the water lowers so air is really needed.

  3. Josh W says

    Hello all, this is a great article with some very good comments that I appreciate. I am still trying to get my feet wet in aquaponics and I have so very many questions, but there is always another opinion out there to counter whatever information I find. I am running a very small 20 gallon rig in my dinning room with goldfish and pepper plants right now just to try to figure things out before I spend any real money on a bigger rig and set of responsibilities.

    All that said, I have asked a lot of people a lot of questions, but answers are few and far between. I have looked for groups in my area (Eastern NC) and have found very little in the way of community. Do you have a suggestion as to where I could look for mentor-ship in this field?

  4. Jerry Nissen says

    Yea Gads! When I first started looking at aquaponics systems,,,,, it was relatively simple, but when trying to establish some basic ground rules: size of grow bed: size of fish tank > number of fish, etc. it all becomes a confusing nightmare – hot much salt, worms, drain / fill cycle…

    I wanted a 4 foot by 6 foot x 1 foot grow bed; guessed at a 4 foot by 6 foot x 1 foot fish tank with a possible 3 foot x 5 foot x 1 foot reservoir – but no one mentioned worms and salt!

    deeply discouraged :-( any hope? : -)

  5. Mark says

    Hi, just started doing a little research on aquaponics today. The advice here seems to be pretty sensible.
    A weak point, from an off-the-grid view, is the high cost of alternative energy infrastructure. Even conventional systems cost electricity. My oddball question is – must the water be recirculated?
    The management of the water condition seems to be key. The water undergoes natural chemical changes as it moves through the system and must be restored to optimum condition when it returns to the first living component, the fish.
    I understand one of the major advantages is water economy but say you had a natural mountain spring of excellent quality water, which downstrean in a dam supports a variety of natural wildlife.
    Say one piped off this spring water and used a valve to adjust the flow and let it fall into the fish tank from a height to create oxygenation. The water then gravitates through the system 24/7 and having transferred the fish nutrients to the plants, at a suitable flow rate, exits the system and returns to the watercourse. (My Evian spring has a flow rate of approximately 1 liter per second.)
    Say the natural incoming water is not optimal for the fishstock, eg Ph, then fittings, such as drip hoppers on the incoming pipeline could be added to adjust the water. I understand very few people have access to mountain springs but could this work?
    I have also heard, in aquaculture, that chickens can be kept above the fish tank and their droppings used to supplement the fish food.Which is cheaper, chicken feed or fish food? Seriously, as a total newbie, I would appreciate any opinions of linear water as opposed to a loop.



    • says

      Hi Mark,

      There is no automatic requirement to recirculate water to grow fish.

      If you have access to a mountain stream or a river, you can do what you describe. Indeed, many trout farms were set up this way. The environmental (and increasingly the moral) issue that presents itself, however, is what happens to the water once it passes through your fish production system.

      If you planned to use it to irrigate pasture or crops then it may (depending on your specific circumstances) be OK. If you intend to re-introduce it into a watercourse, you may find that local environmental authorities will be on your case.

      Regardless of what you might read elsewhere, chicken poop is no substitute for a properly formulated fish ration – and it will aggravate the issues associated with discharging the water back into a watercourse of any kind.

      I appreciate that you are interested in integrated food production, but there are better ways of doing it?

      You’ve raised an interesting question – and one around which there are a variety of options. I’d like to address those other options in a future article.

      In the meantime, keep asking questions.



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