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 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.
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 can cause fish diseases such as:
Parasites in fish are a natural occurrence and common. Parasites can provide information about host population ecology. In fisheries biology, for example, parasite communities can be used to distinguish distinct populations of the same fish species co-inhabiting a region. Additionally, parasites possess a variety of specialized traits and life-history strategies that enable them to colonize hosts. Understanding these aspects of parasite ecology, of interest in their own right, can illuminate parasite-avoidance strategies employed by hosts
Usually parasites (and pathogens) need to avoid killing their hosts, since extinct hosts can mean extinct parasites. Evolutionary constraints may operate so parasites avoid killing their hosts, or the natural variability in host defensive strategies may suffice to keep host populations viable. Parasite infections can impair the courtship dance of male threespine sticklebacks. When that happens, the females reject them, suggesting a strong mechanism for the selection of parasite resistance."
However not all parasites want to keep their hosts alive, and there are parasites with multistage life cycles who go to some trouble to kill their host. For example, some tapeworms make some fish behave in such a way that a predatory bird can catch it. The predatory bird is the next host for the parasite in the next stage of its life cycle. Specifically, the tapeworm Schistocephalus solidus turns infected threespine stickleback white, and then makes them more buoyant so that they splash along at the surface of the water, becoming easy to see and easy to catch for a passing bird.
Other parasitic disorders, include Gyrodactylus salaris, Ichthyophthirius multifiliis, cryptocaryon, velvet disease, Brooklynella hostilis, Hole in the head, Glugea, Ceratomyxa shasta, Kudoa thyrsites, Tetracapsuloides bryosalmonae, Cymothoa exigua, leeches, nematode, flukes, Platyhelminthes, carp lice and salmon lice
Some diseases result in mass die offs. One of the more bizarre and recently discovered diseases produces huge fish kills in shallow marine waters. It is caused by the ambush predator dinoflagellate Pfiesteria piscicida. When large numbers of fish, like shoaling forage fish, are in confined situations such as shallow bays, the excretions from the fish encourage this dinoflagellate, which is not normally toxic, to produce free-swimming zoospores. If the fish remain in the area, continuing to provide nourishment, then the zoospores start secreting a neurotoxin. This toxin results in the fish developing bleeding lesions, and their skin flakes off in the water. The dinoflagellates then eat the blood and flakes of tissue while the affected fish die. Fish kills by this dinoflagellate are common, and they may also have been responsible for kills in the past which were thought to have had other causes. Kills like these can be viewed as natural mechanisms for regulating the population of exceptionally abundant fish. The rate at which the kills occur increases as organically polluted land runoff increases.
Some fish take advantage of cleaner fish for the removal of external parasites. The best known of these are the Bluestreak cleaner wrasses of the genus Labroides found on coral reefs in the Indian Ocean and Pacific Ocean. These small fish maintain so-called "cleaning stations" where other fish, known as hosts, will congregate and perform specific movements to attract the attention of the cleaner fish. Cleaning behaviours have been observed in a number of other fish groups, including an interesting case between two cichlids of the same genus, Etroplus maculatus, the cleaner fish, and the much larger Etroplus suratensis, the host.
More than 40 species of parasites may reside on the skin and internally of the ocean sunfish, motivating the fish to seek relief in a number of ways.  In temperate regions, drifting kelp fields harbour cleaner wrasses and other fish which remove parasites from the skin of visiting sunfish. In the tropics, the mola will solicit cleaner help from reef fishes. By basking on its side at the surface, the sunfish also allows seabirds to feed on parasites from their skin. Sunfish have been reported to breach more than ten feet above the surface, possibly as another effort to dislodge parasites on the body.
According to Canadian biologist Dorothy Kieser, protozoan parasite Henneguya salminicola is commonly found in the flesh of salmonids. It has been recorded in the field samples of salmon returning to the Queen Charlotte Islands. The fish responds by walling off the parasitic infection into a number of cysts that contain milky fluid. This fluid is an accumulation of a large number of parasites.
Henneguya and other parasites in the myxosporean group have a complex lifecycle where the salmon is one of two hosts. The fish releases the spores after spawning. In the Henneguya case, the spores enter a second host, most likely an invertebrate, in the spawning stream. When juvenile salmon out-migrate to the Pacific Ocean, the second host releases a stage infective to salmon. The parasite is then carried in the salmon until the next spawning cycle. The myxosporean parasite that causes whirling disease in trout, has a similar lifecycle. However, as opposed to whirling disease, the Henneguya infestation does not appear to cause disease in the host salmon — even heavily infected fish tend to return to spawn successfully.
According to Dr. Kieser, a big lot of work on Henneguya salminicola was done by scientists at the Pacific Biological Station in Nanaimo in the mid-1980s, in particular, an overview report which states that "the fish that have the longest fresh water residence time as juveniles have the most noticeable infections. Hence in order of prevalence coho are most infected followed by sockeye, chinook, chum and pink." As well, the report says that, at the time the studies were conducted, stocks from the middle and upper reaches of large river systems in British Columbia such as Fraser, Skeena, Nass and from mainland coastal streams in the southern half of B.C. "are more likely to have a low prevalence of infection." The report also states "It should be stressed that Henneguya, economically deleterious though it is, is harmless from the view of public health. It is strictly a fish parasite that cannot live in or affect warm blooded animals, including man".
According to Klaus Schallie, Molluscan Shellfish Program Specialist with the Canadian Food Inspection Agency, "Henneguya salminicola is found in southern B.C. also and in all species of salmon. I have previously examined smoked chum salmon sides that were riddled with cysts and some sockeye runs in Barkley Sound (southern B.C., west coast of Vancouver Island) are noted for their high incidence of infestation."
Sea lice, particularly Lepeophtheirus salmonis and various Caligus species, including Caligus clemensi and Caligus rogercresseyi, can cause deadly infestations of both farm-grown and wild salmon. Sea lice are ectoparasites which feed on mucous, blood, skin, and muscle tissue, and normally latch onto the skin of wild salmon in the open ocean during free-swimming, planktonic naupli and copepodid larval stages, which can persist for several days. Large numbers of highly populated, open-net salmon farms can create exceptionally large concentrations of sea lice; when exposed in river estuaries containing large numbers of open-net farms, many young wild salmon are infected, and do not survive as a result. Adult salmon may survive otherwise critical numbers of sea lice, but small, thin-skinned juvenile salmon migrating to sea are highly vulnerable. On the Pacific coast of Canada, the louse-induced mortality of pink salmon of such affected areas is commonly over 80%.
In 1984, infectious salmon anemia (ISAv) was discovered in Norway in an Atlantic salmon hatchery. Eighty percent of the fish in the outbreak died. ISAv, a viral disease, is now a major threat to the viability of Atlantic salmon farming. It is now the first of the diseases classified on List One of the European Commission’s fish health regime. Amongst other measures, this requires the total eradication of the entire fish stock should an outbreak of the disease be confirmed on any farm. ISAv seriously affects salmon farms in Chile, Norway, Scotland and Canada, causing major economic losses to infected farms. As the name implies, it causes severe anemia of infected fish. Unlike mammals, the red blood cells of fish have DNA, and can become infected with viruses. The fish develop pale gills, and may swim close to the water surface, gulping for air. However, the disease can also develop without the fish showing any external signs of illness, the fish maintain a normal appetite, and then they suddenly die. The disease can progress slowly throughout an infected farm and, in the worst cases, death rates may approach 100 percent. It is also a threat to the dwindling stocks of wild salmon. Management strategies include developing a vaccine and improving genetic resistance to the disease.
In the wild, diseases and parasites are normally at low levels, and kept in check by natural predation on weakened individuals. In crowded net pens they can become epidemics. Diseases and parasites also transfer from farmed to wild salmon populations. A recent study in British Columbia links the spread of parasitic sea lice from river salmon farms to wild pink salmon in the same river." The European Commission (2002) concluded “The reduction of wild salmonid abundance is also linked to other factors but there is more and more scientific evidence establishing a direct link between the number of lice-infested wild fish and the presence of cages in the same estuary.” It is reported that wild salmon on the west coast of Canada are being driven to extinction by sea lice from nearby salmon farms. Antibiotics and pesticides are often used to control the diseases and parasites.
In most aquarium tanks, the fish are at high concentrations and the volume of water is limited. This means that communicable diseases can spread rapidly to 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. Ammonia poisoning is a common disease in new aquariums, especially when immediately stocked to full capacity.
Due to their generally small size and the low cost of replacing diseased or dead aquarium fish, the cost of testing and treating diseases is often seen as more trouble than the value of the fish.
The parasite Henneguya zschokkei in salmon beard
The capture, transportation and culture of bait fish can spread damaging organisms between ecosystems, endangering them. In 2007, several American states, including Michigan, enacted regulations designed to slow the spread of fish diseases, including viral hemorrhagic septicemia, by bait fish. Because of the risk of transmitting Myxobolus cerebralis (whirling disease), trout and salmon should not be used as bait. Anglers may increase the possibility of contamination by emptying bait buckets into fishing venues and collecting or using bait improperly. The transportation of fish from one location to another can break the law and cause the introduction of fish and parasites alien to the ecosystem.
Though not a health concern in thoroughly cooked fish, parasites are a concern when human consumers eat raw or lightly preserved fish such as sashimi, sushi, ceviche, and gravlax. The popularity of such raw fish dishes makes it important for consumers to be aware of this risk. Raw fish should be frozen to an internal temperature of −20°C (−4°F) for at least 7 days to kill parasites. It is important to be aware that home freezers may not be cold enough to kill parasites.
Traditionally, fish that live all or part of their lives in fresh water were considered unsuitable for sashimi due to the possibility of parasites (see Sashimi article). Parasitic infections from freshwater fish are a serious problem in some parts of the world, particularly Southeast Asia. Fish that spend part of their life cycle in brackish or freshwater, like salmon are a particular problem. A study in Seattle, Washington showed that 100% of wild salmon had roundworm larvae capable of infecting people. In the same study farm raised salmon did not have any roundworm larvae.
Parasite infection by raw fish is rare in the developed world (fewer than 40 cases per year in the U.S.), and involves mainly three kinds of parasites: Clonorchis sinensis (a trematode/fluke), Anisakis (a nematode/roundworm) and Diphyllobothrium (a cestode/tapeworm). Infection risk of anisakis is particularly higher in fishes which may live in a river such as salmon (shake) in Salmonidae, mackerel (saba). Such parasite infections can generally be avoided by boiling, burning, preserving in salt or vinegar, or freezing overnight. Even Japanese people never eat raw salmon and ikura, and even if they seem raw, these foods are not raw but are frozen overnight to prevent infections from parasites, particularly anisakis.