Disease cures are almost always more expensive and less effective than simple prevention measures. Often precautions involve maintaining a stable aquarium that is adjusted for the specific species of fish that are kept and not over-crowding a tank or over-feeding the fish. Common preventive strategies include avoiding the introduction of infected fish, invertebrates or plants by quarantining new additions before adding them to an established tank, and discarding water from external sources rather than mixing it with clean water. Similarly, foods for herbivorous fish such as lettuce or cucumbers should be washed before being placed in the tank. Containers that do not have water filters or pumps to circulate water can also increase stress to fish. Other stresses on fish and tanks can include certain chemicals, soaps and detergents, and impacts to tank walls causing shock waves that can damage fish.

Ornamental fish kept in aquariums are susceptible to numerous diseases. Due to their generally small size and the low cost of replacing diseased or dead fish, the cost of testing and treating diseases is often seen as more trouble than the value of the fish.

Due to the artificially limited volume of water and high concentration of fish in most aquarium tanks, communicable diseases often affect most or all fish in a tank. An improper nitrogen cycle, inappropriate aquarium plants and potentially harmful freshwater invertebrates can directly harm or add to the stresses on ornamental fish in a tank. Despite this, many diseases in captive fish can be avoided or prevented through proper water conditions and a well-adjusted ecosystem within the tank.

Velvet (in an aquarium environment) is usually spread by contaminated tanks, fish, and tools (such as nets or testing supplies). There are also rare reports of frozen live foods (such as bloodworms) containing dormant forms of the species. Frequently, however, the parasite is endemic to a fish, and only causes a noticeable "outbreak" after the fish's immune system is compromised for some other reason. The disease is highly contagious and can prove fatal to fish.

The single-celled parasite's life cycle can be divided into three major phases. First, as a tomont, the parasite rests at the water's floor and divides into as many as 256 tomites. Second, these juvenile, motile tomites swim about in search of a fish host, meanwhile using photosynthesis to grow, and to fuel their search. Finally, the adolescent tomite finds and enters the slime coat of a host fish, dissolving and consuming the host's cells, and needing only three days to reach full maturity before detaching to become a tomont once more.

Currently, the most effective treatment is transferring the affected fish to a freshwater bath for a period of 2 to 3 hours. This is achieved by towing the sea cages into fresh water, or pumping the fish from the sea cage to a tarp filled with fresh water. Mortality rates have been lowered by adding Levamisole to the water until the saturation is above 10ppm. Due to the difficulty and expense of treatment, the productivity of salmon aquaculture is limited by access to a source of fresh water. Chloramine and chlorine dioxide have also been used. Other potential in-feed treatments such as immunosupportive-based feeds, mucolytic compounds such as L-cysteine ethyl ester and the parasticide bithionol have been tested with some success although not developed for commercial use.

Quaternary ammonium compounds can be added to the water of infected adult fish and fry. Alternatively, the antibiotic oxytetracycline can be given to adults, fry and broodstock. To prevent the disease, it is necessary to ensure water is pathogen-free and that water hardening is completed effectively for eggs.

Amoebic gill disease (AGD) is a potentially fatal disease of some marine fish. It is caused by "Neoparamoeba perurans", the most important amoeba in cultured fish. It primarily affects farm raised fish of the Salmonidae family, most notably affecting the Tasmanian Atlantic Salmon (Salmo salar) industry, costing the A$20 million a year in treatments and lost productivity. Turbot, bass, bream, sea urchins and crabs have also been infected.

The disease has also been reported affecting the commercial salmon fisheries of the United States, Australia, New Zealand, France, Spain, Ireland and Chile. It was first diagnosed in the summer of 1984/1985 in populations of Atlantic Salmon off the east coast of Tasmania and was found to be caused by the "Neoparamoeba perurans" n.sp.

Bacterial cold water disease (BCWD) is a bacterial disease of salmonid fish. It is caused by "Flavobacterium psychrophilum" (previously classified in the genus "Cytophaga"), a gram-negative rod-shaped bacterium of the family Flavobacteriaceae. The disease typically occurs at temperatures below 13⁰C, and it can be seen in any area with water temperatures consistently below 15⁰C. Salmon are the most commonly affected species. This disease is not zoonotic.

Asymptomatic carrier fish and contaminated water provide reservoirs for disease. Transmission is mainly horizontal, but vertical transmission can also occur.

BCWD may be referred to by a number of other names including cold water disease, peduncle disease, fit rot, tail rot and rainbow trout fry mortality syndrome.

Ulcerations develop within 24 to 48 hours. Fatality occurs between 48 and 72 hours if no treatment is pursued; however, at higher temperatures death may occur within hours. Other symptoms may accompany the disease, including lethargy, color loss, redness around the infection site, loss of appetite and twitching or rubbing the body against objects.

As "Flavobacterium columnare" is Gram-negative, fish can be treated with a combination of the antibiotics furan-2 and kanamycin administered together. A medicated fish bath (using methylene blue or potassium permanganate and salt), is generally a first step, as well lowering the aquarium temperature to 75 °F (24 °C) is a must, since columnaris is much more virulent at higher temperatures, especially 85–90 °F.

Medicated food containing oxytetracycline is also an effective treatment for internal infections, but resistance is emerging. Potassium permanganate, copper sulfate, and hydrogen peroxide can also be applied externally to adult fish and fry, but can be toxic at high concentrations. Vaccines can also be given in the face of an outbreak or to prevent disease occurrence.

Some fish species serve as vectors for the disease and have subsequently spread the pathogen to other parts of the world. An example is the fathead minnow ("Pimephales promelas") which is responsible for the spread of redmouth disease to trout in Europe. Other vectors include the goldfish ("Carassius auratus"), Atlantic and Pacific salmon ("Salmo salar"), the emerald shiner ("Notropis atherinoides"), and farmed whitefish ("Coregonus" spp.). Infections have also occurred in farmed turbot ("Scophthalmus maximus"), seabass ("Dicentrarchus labrax"), and seabream ("Sparus auratus"). It can now be found in North and South America, Africa, Asia, and Australia, as well as Europe.

Several antibiotics are available for the treatment of redmouth disease in fish. Vaccines can also be used in the treatment and prevention of disease. Management factors such as maintaining water quality and a low stocking density are essential for disease prevention.

All fish carry pathogens and parasites. Usually this is at some cost to the fish. If the cost is sufficiently high, then the impacts can be characterised as a disease. However disease in fish is not understood well. What is known about fish disease often relates to aquaria fish, and more recently, to farmed fish.

Disease is a prime agent affecting fish mortality, especially when fish are young. Fish can limit the impacts of pathogens and parasites with behavioural or biochemical means, and such fish have reproductive advantages. Interacting factors result in low grade infection becoming fatal diseases. In particular, things that causes stress, such as natural droughts or pollution or predators, can precipitate outbreak of disease.

Disease can also be particularly problematic when pathogens and parasites carried by introduced species affect native species. An introduced species may find invading easier if potential predators and competitors have been decimated by disease.

Pathogens which can cause fish diseases comprise:

- viral infections, such as esocid lymphosarcoma found in "Esox" species.

- bacterial infections, such as "Pseudomonas fluorescens" leading to fin rot and fish dropsy

- fungal infections

- water mould infections, such as "Saprolegnia" sp.

- metazoan parasites, such as copepods

- unicellular parasites, such as "Ichthyophthirius multifiliis" leading to ich

- Certain parasites like Helminths for example "Eustrongylides"

In Northern Australia, where ciguatera is a common problem, two different folk science methods are widely believed to detect whether fish harbor significant ciguatoxin. The first method is that flies are supposed not to land on contaminated fish. The second is that cats will either refuse to eat or vomit/display symptoms after eating contaminated fish. A third, less common testing method involves putting a silver coin under the scales of the suspect fish. If the coin turns black, according to the theory, it is contaminated.

On Grand Cayman and other islands the locals will test barracuda by placing a piece of the fish on the ground and allowing ants to crawl on it. If the ants do not avoid the flesh and will eat it, then the fish is deemed safe.

In Dominican Republic, another common belief is that during months whose names do not include the letter "R" (May through August), it is not recommended to eat certain kinds of fish, because they are more likely to be infected by the ciguatera toxin.

The validity of many of these tests has been scientifically rejected.

Like humans and other animals, fish suffer from diseases and parasites. Fish defences against disease are specific and non-specific. Non-specific defences include skin and scales, as well as the mucus layer secreted by the epidermis that traps microorganisms and inhibits their growth. If pathogens breach these defences, fish can develop inflammatory responses that increase the flow of blood to infected areas and deliver white blood cells that attempt to destroy the pathogens.

Specific defences are specialised responses to particular pathogens recognised by the fish's body, that is adaptative immune responses. In recent years, vaccines have become widely used in aquaculture and ornamental fish, for example vaccines for furunculosis in farmed salmon and koi herpes virus in koi.

Some commercially important fish diseases are VHS, ich and whirling disease.

Infected fish should be moved into high quality water, where they may recover if their clinical signs are mild.

If disease occurs eradication is required. Once the disease is eradicated good husbandry, surveillance and biosecurity measures are necessary to prevent recurrence. In countries free of epizootic ulcerative syndrome, quarantine and health certificates are necessary for the movement of all live fish to prevent the introduction of the disease.

Fin rot is a symptom of disease or the actual disease in fish. This is a disease which is most often observed in aquaria and aquaculture, but can also occur in natural populations.

Fin rot can be the result of a bacterial infection ("Pseudomonas fluorescens", which causes a ragged rotting of the fin), or as a fungal infection (which rots the fin more evenly and is more likely to produce a white 'edge'). Sometimes, both types of infection are seen together. Infection is commonly brought on by bad water conditions, injury, poor diet, stress, or as a secondary infection in a fish which is already stressed by other disease.

Fin rot starts at the edge of the fins, and destroys more and more tissue until it reaches the fin base. If it does reach the fin base, the fish will never be able to regenerate the lost tissue. At this point, the disease may begin to attack the fish's body; this is called Advanced Fin and Body rot.

Fin rot is common in bettas due to poor water conditions in pet stores.

Various Caribbean folk and ritualistic treatments originated in Cuba and nearby islands. The most common old-time remedy involves bed rest subsequent to a guanabana juice enema. Other folk treatments range from directly porting and bleeding the gastrointestinal tract to "cleansing" the diseased with a dove during a Santería ritual. In Puerto Rico, natives drink a tea made from mangrove buttons, purportedly high in B vitamins, to flush the toxic symptoms from the system. There has never been a funded study of these treatments.

An account of ciguatera poisoning from a linguistics researcher living on Malakula island, Vanuatu, indicates the local treatment: "We had to go with what local people told us: avoid salt and any seafood. Eat sugary foods. And they gave us a tea made from the roots of ferns growing on tree trunks. I don't know if any of that helped, but after a few weeks, the symptoms faded away."

Senescent leaves of "Heliotropium foertherianum" (Boraginaceae), also known as octopus bush, a plant used in many Pacific islands as a traditional medicine to treat ciguatera fish poisoning, contain rosmarinic acid and derivatives, which are known for their antiviral, antibacterial, antioxidant and anti-inflammatory properties. Rosmarinic acid may remove the ciguatoxins from their sites of action, as well as being an anti-inflammatory.

The disruption of olfaction and potential effects to survival and reproductive success at environmentally-relevant concentrations metals, pesticides or surfactants have implications for fish and salmon recovery because these are commonly found in western United States streams. Conventional, acute and chronic toxicity testing do not explicitly address nervous system function and underestimate thresholds for toxicity in salmonids. Since these effects are not explicitly looked at during studies they oftentimes can go unnoticed. Olfactory toxicity occurring at environmentally relevant concentrations can induce reduction to food odor attraction and predator scent or alarm response pheromones can cause major problems with survivorship. Olfactory toxicity can also affect the ability of anadromous fish to find their natal stream causing them to stray to other streams.

Downy mildew refers to any of several types of oomycete microbes that are obligate parasites of plants. Downy mildews exclusively belong to Peronosporaceae. In commercial agriculture, they are a particular problem for growers of crucifers, grapes and vegetables that grow on vines. The prime example is "Peronospora farinosa" featured in NCBI-Taxonomy and HYP3. This pathogen does not produce survival structures in the northern states of the United States, and overwinters as live mildew colonies in Gulf Coast states. It progresses northward with cucurbit production each spring. Yield loss associated with downy mildew is most likely related to soft rots that occur after plant canopies collapse and sunburn occurs on fruit. Cucurbit downy mildew only affects leaves of cucurbit plants.

There is no known cure for little cherry disease and tolerance breeding programs have not yielded any cultivars able to withstand the effects of the disease for more than a few seasons. Thus, prevention of spread has been the focal point in combating the disease.

Long-distance spread of the disease occurs through the planting of infected trees, as well as budding and grafting of infected tissue. To prevent the establishment of the disease, guidelines typically call for testing of rootstocks and budwood before planting, removal of all trees known and suspected to be infected and eradication of ornamental and wild cherry trees from the surrounding area.

Short-distance spread of the disease occurs through transmission of the viruses by insect vectors. Little cherry virus-2 is spread by scale insects of the family Pseudococcidae, primarily the apple mealybug ("Phenacoccus aceris"). In areas where the apple mealybug is commonplace, application of insecticides prior to cutting infected trees are routinely used to stop the spread of little cherry disease within orchards. Little cherry virus-1 is spread by an unknown vector.

Little cherry disease likely originated in Japan and spread with ornamental cherry trees world-wide; many of the top cherry producing nations in the world have reported infections, including USA, Italy and Spain.

Epizootic ulcerative syndrome (EUS), also known as mycotic granulomatosis (MG) or red spot disease (RSD), is a disease caused by the water mould "Aphanomyces invadans". It infects many freshwater and brackish fish species in the Asia-Pacific region and Australia. The disease is most commonly seen when there are low temperature and heavy rainfall in tropical and sub-tropical waters.

Lymphocystis is a common viral disease of freshwater and saltwater fish. The viruses that cause this disease belong to the genus Lymphocystivirus of the family Iridoviridae.

Aquarists often come across this virus when their fish are stressed such as when put into a new environment and the virus is able to grow.

The fish starts growing small white pin-prick like growths on their fins or skin and this is often mistaken for Ich/Ick (Ichthyophthirius multifiliis) in the early stages. It soon clumps together to form a cauliflower-like growth on the skin, mouth, fins, and occasional gills. Lesions at the base of the dorsal fin are common among freshwater species of Central American origin, most notably Herichthys carpentis & inside the mouth of Herichthys cyanoguttatus & Geophagus steindachneri. On the tail fin of Koi, Carps, & US native sunfish (Lepomis sp.) On the side flanks of Walleye, Sauger & Flounder. On random head and/or tail areas of common goldfish, and oranda variants. This virus appears to present itself as a lesion(s) at differing locations depending on the species of fish being attacked, often complicating initial diagnosis.

Lymphocystis does show some host-specificity, i.e., each strain (or species) of lymphocystis can infect only its primary host fish, or some additional closely related, fish.

There is no known cure for this virus, though a privately owned fish research & breeding facility near Gainesville, Florida USA has reportedly been able to suppress the virus into remission using the human antiviral "Acyclovir" at the rate of 200 mg per 10 US gallons for 2 days. Otherwise, some aquarists recommend surgery to remove the affected area if it is very serious, followed by an antibiotic bath treatment to prevent a secondary bacterial infection of the open wounds.

Eventually the growths inhibit the fish's ability to swim, breathe or eat, and secondary bacterial infections usually kills the fish.

Usually the best cure is to simply give the fish a stress free life, a weekly bacteria treatment and the virus will slowly subside and the fins will repair themselves. This can take many months. Like most viral infections, even in humans, the first outbreaks are the most serious, whilst the immune system "learns" how to suppress it, the outbreaks become less severe over time assuming the organism survives the initial outbreaks.

Ulcerative dermal necrosis (UDN) is a chronic dermatological disease of cold water salmonid fish that had a severe impact on north Atlantic Salmon and sea trout stocks in the late 1960s, the 1970s and 1980.

Affected fish developed severe skin lesions over large parts of their body which penetrated into skeletal muscle. The onset of symptoms only occurred after migration into freshwater. Lesions became quickly infected with overgrowths of "Saprolegnia" fungus giving the affected fish an appearance of being covered in slimy white pustules. The most severely affected fish frequently die before spawning.

Although the worst effects of the disease were seen in the 1970s and 1980, even now large numbers of salmon will succumb to the disease after spawning. This is thought be due in part to their weak post-spawning condition, and lack of food for several months whilst in the river.

Those fish that do make it back to the sea are thought to make a good recovery.