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Like other organisms, aquaculture species are susceptible to a number of diseases and parasites such as viruses, bacteria, parasitic protozoans, helmints (worms), copepods and others. When a disease or parasite outbreak occurs in a population of aquatic organisms, it is known not as an epidemic (a term used for the same problem in human populations) but as an epizootic. In most instances, epizootics only result after a population has been stressed.

Stress can occur in a number of ways. If water quality deteriorates, even for a short period, the animals exposed to that water will undergo stress. Handling is another cause of stress in aquaculture species, as are overfeeding or sustained underfeeding. Following exposure to a stressful situation, an epizootic may occur within as little as 24 hours or as long as 2 weeks. The period between the stress episode and the onset of disease or parasite infections depends on the time involved in building the numbers of disease and parasitic organisms to a high level that signs of the disease are observable. Disease and parasite organisms are almost always present in the culture environment, but at very low levels. They only produce disease signs when they are promoted by a lack of resistance in the aquaculture species. An analogy can be drawn in humans. Students in a classroom may be exposed to people with the flu, but not everyone is infected. The immune status of the various individuals play an important role in who will ultimately show flu symptoms. Students who are stressed (for example, by getting too little sleep) are often much more susceptible than those who are not.

The number of chemicals that can be used to treat disease and parasite problems in aquatic animals is small. Only about 10 compounds have been approved for species that are being reared for direct human consumption. Among them few are effective at controlling bacteria, some work on a few parasites but not others, and may are themselves toxic if given in improper doses. Some treatment chemicals are effective when added to the water, but some must be ingested by the aquaculture organisms. Animals that are experiencing disease and parasites problems often refuse to eat, making treatment difficult.

Good overall management of the culture system is perhaps the best way to avoid disease and parasite problems. However, even the best managers experience epizootics on occasion. Treatment chemicals of various kinds should be available, and the culturist should know how to use those chemicals. Chemicals such as antibiotics should not be used routinely, but should be employed when there is a problem requiring treatment, or when there is a very strong probability that a disease and parasite epizootic is imminent.

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