The main purpose of adding salt in Aquaponics is for disease control; salt acts like a natural anti-bacterial agent. In addition, a small amount of salt improves the mucous covering on a fish's body, and this improves the resistance of the fish to diseases and parasites. Salt may also help to prevent fungal infections. If you opt for salt addition, use pure sea salt and avoid table salt. If you can't find any pure sea salt, swimming pool salt is a viable alternative.

However, adding too much salt will kill the fish and stunt plant growth. Therefore, when adding salt, you should do it only in calculated amounts. A good rule of thumb is 1 to 2 ppt (parts per thousand) of salt to water. Some plants and fish will tolerate higher levels, but if you are a novice in Aquaponics systems, you should stick to this amount. Remember, that as time passes, the concentration of salt in the system will change. Evaporation of water, water taken up by the plants, etc... will lead to an increase in salt concentration. It is therefore important that you monitor salt concentration regularly, and you can do so by using an apparatus called a refractometer. You can buy cheap refractometers for just a few dollars and they will do the job.

Many people will have a separate small tank that they use for sick fish, a kind of quarantine tank. This is a good idea as it prevents the spread of disease to other fish and allows you to give medication only to the sick fish and not to the whole system. If you keep such a tank, salt can be very useful, as salt will enhance the fish's immune system. You can use higher concentration of salt in your sick tank - up to 10 ppt for a few hours to a few days. Make sure to keep the tank well oxygenated.

As mentioned already, different fish have different levels of salt tolerance, so to be on the safe side check with your local fisheries department for levels of tolerability of the species you are growing. In addition, remember that even if the fish you are growing are very tolerant to salt (for example tilapia can be grown in a salt concentration of up to 20-30ppt), the plants will not tolerate high concentrations. It is safer if you stick to 1-2ppt.