Like in the fresh or salt water also in the brackish water the fish could become sick. Especially puffers are very susceptible to parasites.
The disease is almost always connected to the weakening of the puffer. Very often the fish are already groggy at the dealer because they are stressed or got thinner due to a long fast or wrong keeping. This leads into an infestation with ichtyopphthirius mulitfilliis (white spotted disease). For the brackish puffers the treatment is relatively easy. Raise the temperature to 30 degrees Celsius, make sure that the oxygen adding is very good and put some artificial sea salt for marine aquarists into the tank. In case of strong infestation a medicinal treatment would be more effective.
On this page you can find an interesting article about Ichthyophthirius.
Furthermore brackish puffers, which are mostly kept in fresh water in the trade, could also get infested by all common diseases and parasites that exist in fresh water.
In this case a rise of the temperature and salt concentration would help, too.
Very important is good oxygen accommodations with a membrane pump or better with a diffuser, that insert the air effectively into the water. Puffers have a higher need of oxygen!
Keeping them you should care for an above-average accommodation of oxygen. It has happened that puffers, being fed just before switching off the light, have died of asphyxiation over night.
The healing of ulcers is much more difficult. There could be many reasons which are complex to find out. In addition there is also a puffer specialized worm parasite that appeared in fresh and brackish water. In the area of ‚€œfresh-water diseases‚€? we dwell on this parasite disease.