For the worm, humans are a dead-end host. "Anisakis" and "Pseudoterranova" larvae cannot survive in humans, and eventually die. In some cases, the infection resolves with only symptomatic treatment. In other cases, however, infection can lead to small bowel obstruction, which may require surgery, although treatment with albendazole alone (avoiding surgery) has been reported to be successful. Intestinal perforation (an emergency) is also possible.

Sodium chloride is believed to mitigate the reproduction of Velvet, however this treatment is not itself sufficient for the complete eradication of an outbreak. Additional, common medications added directly to the fish's environment include copper sulfate, methylene blue, formalin, malachite green and acriflavin, all of which can be found in common fish medications designed specifically to combat this disease. Additionally, because Velvet parasites derive a portion of their energy from photosynthesis, leaving a tank in total darkness for seven days provides a helpful supplement to chemical curatives. Finally, some enthusiasts recommend raising the water temperature of an infected fish's environment, in order to quicken the life cycle (and subsequent death) of Velvet parasites; however this tactic is not practical for all fish, and may induce immunocompromising stress.

Avoid ingestion of raw freshwater fish. Adequate cooking or freezing of freshwater fish will kill the encysted fish tapeworm larvae. Also, because human feces is an important mechanism for spreading eggs, proper disposal of sewage can cut down on infection of fish and thus of humans.

Several public health prevention strategies could help lower the rates of metagonimiasis. One is to control the intermediate host (snails). This can be done through use of molluscidals. Another is to use education to ensure all people, especially in areas were the disease regularly occurs, fully cook all fish. This could potentially be problematic and not as effective as hoped as many of the people affected by metagonimiasis eat raw or pickled fish as part of a traditional, long-seated dietary practice. Additionally, implementing more sanitary water conditions would reduce the continual reintroduction of eggs to water sources, thus restarting the lifecycle. Complete control of metagonimiasis presents several potential problems because it does have several reservoir hosts, thus eradication is unlikely.

Even when the fish is thoroughly cooked, "Anisakis" larvae pose a health risk to humans. Anisakids (and related species such as the sealworm, "Pseudoterranova" species, and the codworm "Hysterothylacium aduncum") release a number of biochemicals into the surrounding tissues when they infect a fish. They are also often consumed whole, accidentally, inside a fillet of fish.

Acute allergic manifestations, such as urticaria and anaphylaxis, may occur with or without accompanying gastrointestinal symptoms. The frequency of allergic symptoms in connection with fish ingestion has led to the concept of gastroallergic anisakiasis, an acute IgE-mediated generalized reaction. Occupational allergy, including asthma, conjunctivitis, and contact dermatitis, has been observed in fish processing workers.

Sensitivization and allergy are determined by skin-prick test and detection of specific antibodies against "Anisakis". Hypersensitivity is indicated by a rapid rise in levels of IgE in the first several days following consumption of infected fish.

Because of Eustrongylides species’ complex life cycle with various host species, preventing infection and controlling outbreaks is difficult. Outbreaks of this disease are closely linked to agricultural runoff and urban development Eutrophication of water bodies supports high population levels of oligochaete worms, which causes increased numbers of infected fish that eat the worms, and then the birds who eat the fish.

One way to prevent Eustrongylidosis is to control oligochaete populations. Outbreaks of this parasite are closely linked to high numbers of oligochaete worms in the area’s waterways. This is because the worms are essential for Eustrongylides species to reproduce. Oligochaete populations can be controlled by monitoring nutrient levels in the water, because high nutrient levels support oligochaete populations. They can also be controlled by decreasing the level of oxygen in the water. Encouraging responsible farming practices in order to reduce chemical run-off will help prevent this disease from occurring.

Managers need to be diligent in catching the symptoms of the parasite before it can become an outbreak. Once an outbreak of Eustrongylidosis has occurred, there is little that ecosystem managers can do to stop the spread in oligochaetes, fish and birds. Traditional anthelminthics (dewormers) are not effective in fish because they kill parasites that live inside the gastrointestinal tract, whereas Eustrongylides species live outside the stomach in the body cavity. The parasites can only be removed from fish surgically, which is not feasible. In order to completely stop the Eustrongylides life cycle in fish, all fish in an affected area must be culled.

Surgical removal of the parasite from wading birds is a viable option, but this would also not be feasible for a large number of birds, and it would not stop the cycle of infection.

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.

In some cases the causes of an infection or disease will be obvious (such as fin rot), though in other cases it may be due to water conditions, requiring special testing equipment and chemicals to appropriately adjust the water. Isolating diseased fish can help prevent the spread of infection to healthy fish in the tank. This also allows the use of chemicals or drugs which may damage the nitrogen cycle, plants or chemical filtration of a properly-functioning tank. Other alternatives include short baths in a bucket that contains the treated water. Salt baths can be used as an antiseptic and fungicide, and will not damage beneficial bacteria, though ordinary table salt may contain additives which can harm fish. Alternatives include aquarium salt, Kosher salt or rock salt. Gradually raising the temperature of the tank may kill certain parasites, though some diseased fish may be harmed and certain species can not tolerate high temperatures. Aeration is necessary since less oxygen is dissolved in warm water.

There are a number of effective treatments for many stains of bacterial infections. Three of the most common are tetracycline, penicillin and naladixic acid. Salt baths are another effective treatment.

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.

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.

Praziquantel is recommended in both adult and pediatric cases with dosages of 75 mg/kg/d in 3 doses for 1 day. Praziquantel is a Praziniozoquinoline derivative that alters the calcium flux through the parasite tectum and causes muscular paralysis and detachment of the fluke. Prizaquantel should be taken with liquids during a meal and as provided commercially as Biltricide. Praziquantel is not approved by the U.S. Food and Drug Administration (FDA) for treatment of metagonimiasis, but is approved for use on other parasitic infections.

Praziquantel has some side effects but they are generally relatively mild and transient and a review of evidence shows it overall a well-tolerated drug. Possible side effects include abdominal pain, allergy, diarrhea, headache, liver problems, nausea or vomiting, exacerbation of porphyries, pruritis, rash, somnolence, vertigo, or dizziness. In fact, in 2002, the World Health Organization recommended the use of Praziquantel in pregnant and lactating women, though controlled trials are still needed to verify this.

Another possible drug option is Tetrachloroethylene, a chlorinated hydrocarbon, but its use has been superseded by new antihelminthic drugs (like Praziquantel). A 1978 study also looked at the efficacy of several drugs on metagonimiasis infection, including bithionol, niclosamide, nicoflan, and Praziquantel. All drugs showed lower prevalence of eggs in feces, however only Praziquantel showed complete radical cure. Therefore, the authors concluded Praziquantel was the most highly effective, was very well tolerated, and was the most promising drug against metagonimiasis.

Surgical removal or treatment with albendazole or ivermectin is recommended.

The most prescribed treatment for gnathostomiasis is surgical removal of the larvae but this is only effective when the worms are located in an accessible location. In addition to surgical excision, albendazole and ivermectin have been noted in their ability to eliminate the parasite. Albendazole is recommended to be administered at 400 mg daily for 21 days as an adjunct to surgical excision, while ivermectin is better tolerated as a single dose. Ivermectin can also serve as a replacement for those that can’t handle albendazole 200 ug/kg p.o. as a single dose. However, ivermectin has been shown to be less effective then albendazole.

Most occurrences are found in areas that lack adequate sanitation and include Southeast Asia, West Africa, and East Africa.

Treatment for Eustrongylidosis is limited in the wading bird population due to the extensive amount of perforation in the stomach lining and limited funds available for treatment. In humans who are infected with Eustrongylidosis, surgery is required to remove the parasite from the intestinal wall. As surgery is not a feasible treatment option for wading fowl in the wild "en masse", treatment of the infected birds (a large portion of wild populations) has not been found, nor will likely be practical. There is the possibility that killing/removing the nematodes could do more harm to the host specimen than actual good.

Upon diagnosis, treatment is quite simple and effective. The standard treatment for diphyllobothriasis, as well as many other tapeworm infections is a single dose of praziquantel, 5–10 mg/kg orally once for both adults and children. An alternative treatment is niclosamide, 2 g orally once for adults or 50 mg/kg (max 2 g) for children. Praziquantel is not FDA-approved for this indication and niclosamide is not available for human or even animal use in the United States. Reportedly, albendazole can also be effective. Another interesting potential diagnostic tool and treatment is the contrast medium, Gastrografin, introduced into the duodenum, which allows both visualization of the parasite, and has also been shown to cause detachment and passing of the whole worm.

Effective prevention could be readily achieved by persuading people to consume cooked fish (via education programs), but the ancient cultural custom to consume raw, undercooked or freshly pickled fish persists in endemic areas. One community health program, known as the "Lawa" model, has achieved success in the Lawa Lakes region south of Khon Kaen. Currently, there is no effective chemotherapy to combat cholangiocarcinoma, such that intervention strategies need to rely on the prevention or treatment of liver fluke infection/disease.

Cooking or deep-freezing (-20 °C for 7 days) of food made of fish is sure method of prevention. Methods for prevention of "Opisthorchis viverrini" in aquaculture fish ponds were proposed by Khamboonruang et al. (1997).

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.

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.

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.

Anthelmintics such as mebendazole and albendazole have been reported to eliminate infestation of humans more effectively than thiabendazole.

Prevention is as simple as avoiding eating small, whole, uncooked fish. However, in "C. philippinensis" endemic areas, such dietary habits are common and have been practiced for many generations.

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.

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 salt water, like salmon, can also be a 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 by the fish tapeworm "Diphyllobothrium latum" is seen in countries where people eat raw or undercooked fish, such as some countries in Asia, Eastern Europe, Scandinavia, Africa, and North and South America. 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 or ikura (salmon roe), and even if they seem raw, these foods are not raw but are frozen overnight to prevent infections from parasites, particularly anisakis.

Below are some life cycles of fish parasites that can infect humans:

Chloroquine was used unsuccessfully in attempts to treat opisthorchiasis in 1951-1968. Control of opisthorchiasis relies predominantly on antihelminthic treatment with praziquantel. The single dose of praziquantel of 40 mg/kg is effective against opisthorchiasis (and also against schistosomiasis). Despite the efficacy of this compound, the lack of an acquired immunity to infection predisposes humans to reinfections in endemic regions. In addition, under experimental conditions, the short-term treatment of "Opisthorchis viverrini"-infected hamsters with praziquantel (400 mg per kg of live weight) induced a dispersion of parasite antigens, resulting in adverse immunopathological changes as a result of oxidative and nitrative stresses following re-infection with "Opisthorchis viverrini", a process which has been proposed to initiate and/or promote the development of cholangiocarcinoma in humans. Albendazole can be used as an alternative.

A randomised-controlled trial published in 2011 showed that the broad-spectrum anti-helminthic, tribendimidine, appears to be at least as efficacious as praziquantel. Artemisinin was also found to have anthelmintic activity against "Opisthorchis viverrini".

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.

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.