Starting an aquaponic system is a lot like juggling in a circus: there are a lot of balls in the air, and you have to collect them in the correct order. Unfortunately, one of the things often forgotten in our frantic efforts to get everything right is that we are placing fish in a system that recirculates water, and the diseases along with it.

Note: I am not an infectious disease expert, or anything remotely close. As a consequence, I will keep this fairly high level.

Because our water is being recirculated repeatedly in an aquaponic system, the disease don't just wash down stream with the water, but rather are reintroduced to the same fish over and over. This is a bit like a day care center where the diseases are passed around between the kids in a vicious circle. Since we have no easy way to stop the diseases once started without severely disrupting the whole system, it is absolutely essential that we deal with the problem before it becomes a problem.

While I am certain there are a nearly infinite number of diseases that can affect your fish, there are really only a few that occur repeatedly and regularly in my experience. The two biggest problems are easily Columnaris, and ICH.

When you get new fish (new to you), I highly recommend treating them for both of these problems immediately. I have lost thousands of fish learning this lesson. If you don't want to treat the fish without first seeing the disease, your only other alternative is to isolate the new fish in a tank where you can easily inspect them without stressing them out. Keep them there for 20 days under observation. If any fish dies or behaves oddly, you should investigate immediately. Be prepared to treat the fish since they will likely all die in the time it takes to ship a treatment.

Columnaris is technically a symptom (as noted by the Wikipedia page linked above), but it is the term commonly used to refer to the bacterial infection. You should assume that any fish you get from an external source is infected by this bacteria because you will have a difficult time combating it once it is clear that you have a problem. Unfortunately this problem can only be dealt with by bathing your fish in antibiotics. Specifically you will need to obtain Furan-2. There may be other antibiotics that work - but this is the one I have successfully used many times. I don't recall the exact details, but expect treatment to take roughly 10 days in an isolated tank with a minimal amount of water which is replaced regularly and heavily oxygenated.

ICH fortunately is much easier to deal with, but it is also much more likely your new fish will be carrying it. Always treat for ICH! Treatment is to isolate your fish and dose the water with salt. Specifically you are looking for sodium chloride (NaCl) with no additives. You want 3 parts per thousand (ppt) MORE salt than was already in the water the fish were previously living in. This means adding 3 grams salt per liter of water, or roughly 2 teaspoons per gallon of water. For scaled fish this is generally not a problem, but going over 5 ppt salt for scaleless fish like Catfish is very iffy (watch for signs of stress such as gasping at the surface). ICH is a parasite that has a cycle where it spends part of the cycle floating free in the water. It is during this part of the cycle that the salt will likely kill it. To speed up the cycle so that your fish survive and you don't have to treat for ever, you need to increase the temperature of the water to an ideal temperature of 86° F (84-88). If you are like me, and live in a colder climate, I strongly suggest you consider waiting until summer to purchase your fish. Also get them young so they don't require a large treatment tank. These tips will avoid the need for a whole lot of electricity.

A few thoughts & tips:

  • There is at least one strain of ICH that is salt resistant (or immune?). The advice I have seen is to simply let the fish die in this event.
  • I have tried various alternative ICH treatments. They are no better than salt, and may be a fair bit worse if they don't eradicate the ICH entirely.
  • ICH will not occur in your system unless it is introduced with fish or plants.
  • I have not seen any evidence that Columnaris will occur without an introduction of diseased fish (plants cannot carry this one).
  • Never share water between systems. Never.
  • At a minimum, you should always keep new (to you) fish separate for at least 10 days (two weeks is advisable) to observe them. If they are dying, don't put them in your system without first determining the cause and fixing it.
  • Don't even consider using a solar water heating setup to avoid electric usage. Solar is not a substitute for a good water heater because it is not easily controllable, and the heat loss at night will create such wild temperature fluctuations that you fish won't need a disease to die.
  • I don't ever recommend treating your fish in your aquaponic system. Always use a separate tank where you can easily replace the water, maintain an optimal temperature, and observe the fish without causing undue stress (don't catch them repeatedly to look at them).
  • Running salt in your system as a means of preventing disease is neither necessary or wise.
  • Keep your aquaponic system's bacteria going during extended fish-less periods by adding some ammonia. I have used cheap ammonia sold by the gallon at Ace Hardware - you will really only need a small amount.
  • There are options for converting ammonia and nitrites into nitrates using chemicals that are not affected by bacteria killing treatments. Using these may reduce the number of water changes you need. I have never had occasion to try them since I try to plan my intake of new fish to when I have an excess of water.
  • Fish hatcheries are not supposed to ship diseased fish, and they will always deny doing it to their dying breath. Unfortunately that is not reality. I have not yet taken any fish in from a hatchery that did not have at least one nasty disease.
  • Pool salt with NO additives is a good source of salt for treating ICH. Walmart in the US has the best prices on a quality pool salt, if you can stomach shopping there.
  • Purchase extra nets so you never use nets (or any other equipment) from one system in another system. Nets used with sick fish should ideally never be used in a clean tank, but should either be sterilized with hot water or left dry for 30 days. Diseases like ICH can easily pass from one system to another on equipment.