Treatments are anything that’s not fish food that you apply to either the aquarium, fish or the plants. For our purposes here, it can be medicine for the fish or plants, water conditioners, plant sprays, pesticides, fungicides, fertilizers, and possibly the ‘stuff’ you put into filters and grow beds if it’s intended to modify the water in some way.

There are three things to keep in mind when deciding to use a treatment, and what treatment to use beyond whether or not it does what it’s supposed to do.

  • What does it do to the aquarium & fish?
  • What does it do to the plants?
  • What does it do to humans?

Lets start with a few basic assumptions.

  • We plan on eating the plants we grow.
  • We don’t plan on eating the fish. is focused on growing plants out of aquariums. Most aquariums are not large enough to grow fish to sizes that are large enough for most people to bother eating them, so we’ll not worry about eating the fish. Both edible and ornamental plants can be grown in the hydroponics half of the aquaponics system, but it appears the bulk of the interest is in edible plants. Things that are bad for plants will generally be bad for both edible and ornamental plants. You don’t want to put anything into the system that is bad for humans if you plan on eating anything from the aquaponics system.

Read the Labels

The first thing to do is to read the labels. On most of the medicines, drops, etc. for an aquarium and aquarium fish, they say “For ornamental fish use Only” – you don’t want to use these if you plan on eating anything from the system. If you look at many of the sprays for plants, they say “May be toxic or harmful to fish” – you don’t want to use these either.


Organic is good, right? An aquaponic system tends to be nearly organic if not true organic simply because a lot of the traditional non-organic treatments aren’t safe for both plants and fish.

Just because something is organic, doesn’t mean that it’s inherently safe for an aquaponics system. A ‘100% Organic’ poison is still a poison.

If given a choice between organic and non-organic, personally, I would choose the organic – all things being nearly equal. Be sure to read the labels on the organic stuff too.


If you do need to treat an individual or few specimens, it can be beneficial to do it in a separate system. You can move fish to a quarantine tank, and plants to a small, more traditional hydroponics system. These separate systems can be much smaller then the main system, so you need to use less treatment, which should save you money. The treatment system should be of a well known size e.g. a 10 gallon aquarium or 20 gallon hydroponics system, which makes dosing much simpler and more accurate. Maybe more interestingly, you can uncouple the aquaponics system into separate aquarium and hydroponics systems, reducing the potential side effects of a treatment. You’ve not only removed the disease from your running aquaponics system, you can now use treatments that incompatible with an aspect of a whole aquaponics system.

By treating fish in ‘just an aquarium’, you can use standby treatments such as salt, or many fish medications that are toxic to plants. You also don’t have to worry about the plants ‘sucking up’ all the medicine before it gets a chance to work on the fish. Moving plants to a traditional hydroponics setup, you can use sprays and treatments that are harmful to fish or may upset the balance to the system. You could also manipulate the hydroponic solutions as a diagnostic tool to identify potential deficiency in the aquaponics system as a whole without fear of ‘spoiling’ the system.

There are a few ways to run isolation systems. One is to have them always available – already running, or ready to run. Another is to have duplicate ‘key’ components for a system running in the main system, and move them over to the isolation system when in need. Or, for many people, you have to go get what you need, or otherwise ‘make it work’.

Quarantine Tanks

A quarantine tank is an aquarium set up to hold any sick or new fish. You remove any sick fish from your existing aquarium and put them into the quarantine tank, or put any new fish into it for a couple of weeks before adding them to your aquarium.

Some aquarium treatments have different dosing for different types of fish. For example, the Tetra group of fish should only be dosed at half strength for some types of Ich medications – the instructions on the bottle will tell you this. By moving non-tetras away from the tetras, you can dose at full strength. Some treatments are toxic to arthropods or mollusks – if you use them in your main aquarium, they will kill your shrimp or snails.

If you are running a lot of aquariums or have expensive fish, you probably already have a dedicated quarantine tank running all the time. This option is for the dedicated aquarist.

My preferred method of having a Quarantine tank is to store my 10 gallon tank away, but have that tank’s filter equipment running in my main system. I have this running on a separate surge strip so if I ever blow a surge strip breaker, I have a backup filter running to keep some water circulation in my main tank (you could put this on a battery backup if your really paranoid). If/when I need the isolation tank, I dig it out, set it on a table, transfer 10 gallons of water from the main tank into the quarantine tank & move the small filter to the sick tank. I now have a fully cycled, running 10 gallon tank with the exact same water conditions as the main tank. I move the fish that need to be moved, and apply the necessary treatments. Any treatment prescribed water changes get drawn off the main tank into the sick tank. This keeps the sick tank water conditions very close to the main tank so that you can net the fish out of the quarantine tank and dump them into the main tank without much fear of shock or needing to ‘float’ the fish.

When the treatment period is all over and the fish have been moved back to the main tank, I break the sick tank down and clean it well. The filter media is tossed. Then the filter and tank get scrubbed with bleach and rock salt and rinsed very well. Remember, bleach kills fish. New filter media is put into the filter, and that gets set back up on the main tank which will speed-cycle the filter. The tank gets put away.

If you feel the need to go out and get something to use as a quarantine tank, a 10 gallon ‘all in one’ kit would be my recommendation. With that being said, I’ve used an old ice-chest/cooler and plastic totes. If you use a tote with a narrow rim on the top, you can pick up a cheap over-the-side hanging filter which will hang on the tote just fine. The tote can be used for both your quarantine aquarium and quarantine hydroponics system. Use the same process of pulling water out of the main tank into the quarantine setup.

Quarantine Hydroponics

Why would you want to quarantine a plant? There are several reasons, from diseases spreading between plants faster in a closed loop hydroponics system to specific treatments being harmful to fish. Removing a heavily bug infested plant away from close proximity to other plants or even out of the house will help keep the nasty little critters from jumping to your other plants quickly while you treat them. Using sprays that are toxic to fish can be difficult to keep the over-spray from settling into grow-beds and nearby aquariums, poisoning the fish.
Plant quarantine can be a chore. Plants simply are not as mobile as fish are. However, if you design your system with the potential need to isolate plants in mind, you can make the job much easier.

Plants grown using a particular hydroponics method probably ought to be isolated into the same type of system. Transitioning from one method to another can be stressful to a plant under ideal circumstances. It would be bad for the plant to induce that additional stress burden while the plant is already stressed.

As you venture into the world of aquaponics, you are likely to play with a bunch of different methods and equipment before you settle on what works well for you, your space, and your plants and fish. AquariPonics, by the nature of being in the house or office and being on display has that extra aesthetic component. You’ll probably try to find something that works, and then make that again so it looks good as well. Keep that previous generation of ‘stuff’, as you can use it for your quarantine equipment. This can range from pumps that are too small or noisy, air-stones that broke or are too big, trays that are scratched, dented, or have 1 too many holes drilled into the wrong side of them. You can use all of this gear to rig up a temporary home for your plants.

Having separated your plants from your aquaponics system as a whole, you are going to need to use traditional hydroponics fertilizer supplies. If you augment your main system with hydroponic fertilizers, you may have all you need already. Otherwise you may need to acquire the fertilizers you need.

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