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.

The main symptoms are diarrhea and colicky abdominal pain. Because symptoms are often mild, infections can often be easily overlooked but diagnosis is important. Flukes attach to the wall of the small intestine, but are often asymptomatic unless in large numbers. Infection can occur from eating a single infected fish source. Peripheral eosinophilia is associated especially in early phase. When present in large numbers, can cause chronic intermittent diarrhea, nausea, and vague abdominal pains. Clinical complaints can also include lethargy and anorexia. In acute metagonimiasis, clinical manifestations are developed only 5–7 days after infection. Heavy infection has also been associated with epigastric distress, fatigue, and malaise.

Occasionally, flukes invade the mucosa and eggs deposited in tissue may gain access to circulation. This can then lead to eggs embolizing in the brain, spinal cord, or heart. Granulomas may form around eggs and can cause seizures, neurologic deficits, or cardiac insufficiency.

An interesting case in Japan found Diabetes Mellitus (DM) to be a sign of chronic infection with intracerebral hemorrhages as the acute sign of aggravation. Two months after administering the appropriate drug, Praziquantel, the ICHs were gone, as was the man's Diabetes Mellitus. This unique case shows the potential of additional symptoms associated with metagonimiasis that are still unknown.

Eustrongylidosis is a parasitic disease that mainly affects wading birds worldwide; however, the parasite’s complex, indirect life cycle involves other species such as aquatic worms and fish. Moreover, this disease is zoonotic which means the parasite can transmit disease from animals to humans. Eustrongylidosis is named after the causative agent Eustrongylides and typically occurs in eutrophicated waters where concentrations of nutrients and minerals are high enough to provide ideal conditions for the parasite to thrive and persist. Because eutrophication has become a common issue due to agricultural runoff and urban development, cases of Eustrongylidosis are becoming prevalent and hard to control. Eustrongylidosis can be diagnosed before or after death by observing behavior, clinical signs and performing fecal flotations and necropsies. Methods to control Eustrongylidosis include preventing eutrophication and providing hosts with uninfected food sources in aquaculture farms. Parasites are known to be indicators of environmental health and stability and should therefore be studied further to better understand the parasite’s life cycle and how it affects predator-prey interactions and improve conservation efforts.

Anisakis is a genus of parasitic nematodes, which have lifecycles involving fish and marine mammals. They are infective to humans and cause anisakiasis. People who produce immunoglobulin E in response to this parasite may subsequently have an allergic reaction, including anaphylaxis, after eating fish infected with "Anisakis" species.

A few days after ingestion epigastric pain, fever, vomiting, and loss of appetite resulting from migration of larvae through intestinal wall to the abdominal cavity will appear in the patient. Migration in the subcutaneous tissues (under the skin) causes intermittent, migratory, painful, pruritic swellings (cutaneous larva migrans). Patches of edema appear after the above symptoms clear and are usually found on the abdomen. These lesions vary in size and can be accompanied by pruritus, rash, and stabbing pain. Swellings may last for 1 to 4 weeks in a given area and then reappear in a different location. Migration to other tissues (visceral larva migrans), can result in cough, hematuria, ocular (eye) involvement, meningitis, encephalitis and eosinophilia. Eosinophilic myeloencephalitis may also result from invasion of the central nervous system by the larvae.

Diphyllobothriasis is the infection caused by tapeworms of the Diphyllobothrium genus, commonly "Diphyllobothrium latum" and "Diphyllobothrium nihonkaiense".

Gnathostomiasis (also known as larva migrans profundus) is the human infection caused by the nematode (roundworm) "Gnathostoma spinigerum" and/or "Gnathostoma hispidum", which infects vertebrates.

The genus "Anisakis" was created in 1845 by Félix Dujardin as a subgenus of the genus "Ascaris" Linnaeus, 1758. Dujardin did not make explicit the etymology, but stated that the subgenus included the species in which the males have unequal spicules (""mâles ayant des spicules inégaux""); thus, the name "Anisakis" is based on "anis-" (Greek prefix for different) and "akis" (Greek for spine or spicule). Two species were included in the new subgenus, "Ascaris (Anisakis) distans" Rudolphi, 1809 and "Ascaris (Anisakis) simplex" Rudolphi, 1809.

Velvet disease (also called gold-dust, rust and coral disease) is a fish disease caused by dinoflagellate parasites of the genus "Piscinoodinium", specifically "Amyloodinium" in marine fish, and "Oodinium" in freshwater fish. The disease gives infected organisms a dusty, brownish-gold color. The disease occurs most commonly in tropical fish, and to a lesser extent, marine aquaria.

Diphyllobothriasis can last for decades if untreated. Most infections are asymptomatic. Manifestations may include abdominal discomfort, diarrhea, vomiting and weight loss. Vitamin B12 deficiency with subsequent megaloblastic anemia may occur, but has not for several decades in "D. latum" infections, possibly because of improved nutrition. In one test, nearly half of the ingested vitamin was absorbed by "D. latum" in otherwise healthy patients, while 80-100% was absorbed by the worm in patients with anemia. It is not known why anemia occurs in some cases but not others. Massive infections may result in intestinal obstruction. Migration of proglottids can cause cholecystitis or cholangitis.

Females cases are disproportionately reported, most likely due to the higher likelihood for them to be involved in meal preparation, rather than any morphological differences.

Metagonimiasis is a disease caused by an intestinal trematode, most commonly "Metagonimus yokagawai", but sometimes by "M. takashii" or "M. miyatai". The metagonimiasis-causing flukes are one of two minute flukes called the heterophyids. Metagonimiasis was described by Katsurasa in 1911–1913 when he first observed eggs of "M. yokagawai" in feces (date is disputed in various studies). "M. takahashii" was described later first by Suzuki in 1930 and then "M. Miyatai" was described in 1984 by Saito.

Stained adult fluke causing metagonimiasis

Although tapeworms in the intestine usually cause no symptoms, some people experience upper abdominal discomfort, diarrhea, and loss of appetite. Anemia may develop in people with the fish tapeworm. Infection is generally recognized when the infected person passes segments of proglottids in the stool (which look like white worms), especially if a segment is moving.

Rarely, worms may cause obstruction of the intestine, and very rarely, T. solium larvae can migrate to the brain causing severe headaches, seizures and other neurological problems. Neurocysticercosis can progress for years before the patient displays symptoms.

In at least one case, cancer cells from a tapeworm spread to the human host in an immunocompromised man, producing swelling, obstructions, and other conventional symptoms of human-originated cancer.

Diagnosis usually involves finding the eggs and/or adults of "C. philippinensis" in stool samples.

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.

Infection can cause subcutaneous haemorrhage that presents as reddening of the throat, mouth, gill tips, and fins, and eventual erosion of the jaw and palate. Hemorrhaging also occurs on internal organs, and in the later stages of the disease, the abdomen becomes filled with a yellow fluid - giving the fish a "pot-bellied" appearance. The fish often demonstrate abnormal behavior and anorexia. Mortality rates can be high.

A presumptive diagnosis can be made based in the history and clinical signs, but definitive diagnosis requires bacterial culture and serological testing such as ELISA and latex agglutination.

Clonorchiasis is an infectious disease caused by the Chinese liver fluke, "Clonorchis sinensis", and two related species.

Clonorchiasis is a known risk factor for the development of cholangiocarcinoma, a neoplasm of the biliary system.

Symptoms of opisthorchiasis caused by "Opisthorchis viverrini" and by "Opisthorchis felineus" are indistinguishable from clonorchiasis caused by "Clonorchis sinensis", so the disease by these three parasites should be referred as clonorchiasis.

Capillariasis is a disease in the group of helminthiasis diseases caused by the nematode "Capillaria philippinensis".

Tapeworm infection is the infestation of the digestive tract by a species of parasitic flatworm (known as a cestode), called tapeworms. Live tapeworm larvae grouped in cysts (coenuri)are sometimes ingested by consuming undercooked meat. Once inside the digestive tract, a larva can grow into a very large adult tapeworm. Additionally, many tapeworm larvae cause symptoms in an intermediate host. For example, cysticercosis is a disease involving larval tapeworms in the human body.

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.

Eustrongylidosis is caused by several species of roundworms. The nematodes are red, large, and easily noticeable and are characterized by the absence of a posterior sucker. These roundworms cause a high mortality rate in nesting egrets and other wading birds, including other coastal populations. The parasite was first detected in fish. The parasite is then transferred from the fish to the waterfowl when the bird is eating the fish. After consumption, the parasite perforates through the stomach lining often resulting in the death of the host.

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"

Fish infected with typical BCWD have lesions on the skin and fins. Fins may appear dark, torn, split, ragged, frayed and may even be lost completely. Affected fish are often lethargic and stop feeding. Infection may spread systemically. Salmonid fish can also get a chronic form of BCWD following recovery from typical BCWD. It is characterised by erratic “corkscrew” swimming, blackened tails and spinal deformities.

In rainbow trout fry syndrome, acute disease with high mortality rates occurs. Infected fish may show signs of lethargy, inappetance and exopthalmos before death.

A presumptive diagnosis can be made based on the history, clinical signs, pattern of mortality and water temperature, especially if there is a history of the disease in the area. The organism can be cultured for definitive diagnosis. Alternatively, histology should show periostitis, osteitis, meningitis and ganglioneuritis.

Symptoms of opisthorchiasis (caused by "Opisthorchis" spp.) are indistinguishable from clonorchiasis (caused by "Clonorchis sinensis"). About 80% of infected people have no symptoms, though they can have eosinophilia. Asymptomatic infection can occur when there are less than 1000 eggs in one gram in feces. Infection is considered heavy when there are 10,000-30,000 eggs in one gram of feces. Symptoms of heavier infections with "Opisthorchis viverrini" may include: diarrhoea, epigastric and upper right quadrant pain, lack of appetite (anorexia), fatigue, yellowing of the eyes and skin (jaundice) and mild fever.

These parasites are long-lived and cause heavy chronic infections that may lead to accumulation of fluid in the legs (edema) and in the peritoneal cavity (ascites), enlarged non-functional gall-bladder and also cholangitis, which can lead to periductal fibrosis, cholecystitis and cholelithiasis, obstructive jaundice, hepatomegaly and/or fibrosis of the periportal system.

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.

Diseases can have a variety of causes, including bacterial infections from an external source such as "Pseudomonas fluorescens" (causing fin rot and fish dropsy), fungal infections (Saprolegnia), mould infections (Oomycete and "Saprolegnia"), parasitic disorders ("Gyrodactylus salaris", "Ichthyophthirius multifiliis", Cryptocaryon, Oodinium causing velvet disease, "Brooklynella hostilis", head and lateral line erosion, Glugea, "Ceratomyxa shasta", "Kudoa thyrsites", "Tetracapsuloides bryosalmonae", "Ceratomyxa shasta" leeches, nematode, Trematoda, Platyhelminthes and fish louse), viral disorders, metabolic disorders, inappropriate water conditions (insufficient aeration, pH, water hardness, temperature and ammonia poisoning) and malnutrition.

External bacterial infections may cause spots or streaks on the body which appear red or orange Dropsy (bloating) is also a sign of a bacterial infection. "False fungal infections" look like fungus but is actually a bacterial infection known as Columnaris. These symptoms may include a white or gray film on the body.