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.

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.

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.

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.

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.

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.

There is no effective treatment or antidote for ciguatera poisoning. The mainstay of treatment is supportive care. There is some evidence that calcium channel blockers like nifedipine and verapamil are effective in treating some of the symptoms that remain after the initial sickness passes, such as poor circulation and shooting pains through the chest. These symptoms are due to the cramping of arterial walls caused by maitotoxin Ciguatoxin lowers the threshold for opening voltage-gated sodium channels in synapses of the nervous system. Opening a sodium channel causes depolarization, which could sequentially cause paralysis, heart contraction, and changing the senses of hot and cold. Some medications such as amitriptyline may reduce some symptoms, such as fatigue and paresthesia, although benefit does not occur in every case.

Mannitol was once used for poisoning after one study reported symptom reversal. Follow-up studies in animals and case reports in humans also found benefit from mannitol. However, a randomized, double-blind clinical trial found no difference between mannitol and normal saline, and based on this result, mannitol is no longer recommended.

Long term management of chronic Ciguatera includes avoiding trigger food and environmental triggers, and managing symptoms with medications and or lifestyle.

Caution may be needed with anesthesia and should be discussed with your healthcare providers.

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.

Strawberry foliar nematodes are difficult to manage due to their robust life cycle. While dormant, they are quite difficult to kill, and they remain viable in dry debris for more than one year. Adult nematodes can survive desiccation and lie dormant for several years. Eggs can stay dormant until survival conditions are optimal for growth. Once eggs or nematodes are present in the soil, they are nearly impossible to eradicate because they can move laterally in the soil to escape non-optimal conditions. They are found in most foliar tissue, including the leaves, stems, buds, and crowns, making it difficult to control the disease on the plant itself once it has been infected

Many plant diseases are managed chemically, but due to a ban of nematicides there are currently no nematicides available for any type of foliar nematode. Some insecticides, pesticides, and plant product extracts from plants such as Ficus and Coffee (of which many pesticides and nematicides are neem-based ) can be used to reduce the numbers of strawberry foliar nematode (a reduction of 67-85%), but none of these chemicals can completely eradicate the nematodes once they are present in the soil. These chemicals affect all stages of the life cycle because they target the nervous system. One chemical, ZeroTol, a broad-spectrum fungicide and algaecide, was shown be to 100% potent against nematodes living in a water suspension, but the study does not show how nematodes are affected in soil or outside of a laboratory environment.

An alternative method of control is a hot water treatment, which affects all stages of the life cycle and can be used on whole plants. This treatment has been used for 60 years with some effect in greenhouse plants, but not on a widespread agricultural level. The difficulty in this treatment is that exposure times to hot water and the temperature of the water must be optimized so that the nematodes are killed, but the cultivar remains undamaged. One study, which researched five California strawberry cultivars including Chandler, Douglas, Fern, Pajaro, and Selva, demonstrated that the minimum-maximum exposure times and temperatures that killed the nematodes but did not harm the cultivars were: 20–30 minutes at 44.4⁰C, 10–15 minutes at 46.1⁰C, and 8–10 minutes at 47.7⁰. The study also found that fruit production was more sensitive to the treatment than mere survival of the plant, so the minimum exposure times are recommended when using plants for fruit production, and the maximum time is recommended when using plants for propagation.

One of the best and most practiced forms of management to reduce the local and geographical spread of the disease is sanitation. Removing the infected leaves of the plant can reduce spread in the individual plant, but because the nematode is found in most foliar tissue the nematodes may already be present in other tissues before the leaf symptoms appear. The nematodes can also move on the outside of the plant surface when water is present, so the nematodes can move around the outside surface of the plant and infect new tissues. Therefore, once plants show any signs of infection, they should be removed and destroyed. Reducing or eliminating overhead irrigation can prevent dispersal of the nematode through water splashing, and keeping the foliage dry prevents the nematodes from moving on the outside of the plant. Plants should be placed further apart to allow water to dry quickly after irrigation. In the greenhouse or nursery, soils, containers, and tools should be sterilized on a regular basis, and the floor and storage areas should be free from plant debris.

The most important form of management is prevention of introduction of the nematode to the environment. One should avoid planting infected plants, and it is recommended that new plants (especially in a personal lawn or greenhouse) be planted in an isolated area to monitor the plant for the development of symptoms before transplanting the plant near established plants. This will prevent the established plants from getting infected from a new, infected plant. All symptomatic plants should be destroyed immediately. Dead plant material should also be handled with caution. Vermiform nematodes can survive and reproduce in compost piles of dead plant material by feeding on fungi that are commonly found in compost. As a result, infected plants should be burned and sterilized to prevent the nematodes from infecting soil (which results directly from burying the material), or other plants (from allowing the plant to remain rooted in the soil near other plants as it dies).

Extensive treatments have been used on domestic animals more than on wild animals, probably because infected domestic animals are easier to identify and treat than infected wildlife. Treatment plans and management vary across taxa because this disease tends to affect each species differently. Antifungal drugs are the first line of defense to kill the agents causing phaeohyphomycosis, but despite the significant progress made in the last two decades and a 30% increase in available antifungal drugs since 2000, many drugs are not effective against black fungi. Diseases caused black fungi are hard to treat because the fungi are very difficult to kill. This high resilience may be contributed to the presence of melanin in their cell walls. Current antifungal agents the fungi are not resistant to are posaconazole, voriconazole, and azole isavuconazole.

In 2006, a free-living Eastern box turtle, "Terrapene carolina carolina", was found with a form of phaeohyphomycosis and was brought in the Wildlife Center of Virginia. Its symptom was swelling of the right hindfoot; it was diagnosed as having chromomycosis by histopathology. The center provided a series of antimicrobial treatments and a one-month course of 1 mg itraconazole, administered orally once a day. The eastern box turtle was euthanized due to further complications and the caretakers’ belief that the turtle would not be able to survive if placed back in the wild.

A recent case of a form of phaeohyphomycosis infection was found in a dog in 2011. The Journal of the American Veterinary Medical Association published a case study in which researchers successfully managed an intracranial phaeohyphomycotic fungal granuloma in a one-year-old male Boxer dog. Veterinarians of the Department of Veterinary Clinical Sciences at Tufts University surgically removed the granuloma in the right cerebral hemisphere. The patient was treated with fluconazole for 4 months, and was followed with voriconazole for 10 months. Both are medications used to treat fungal infections. Based on magnetic resonance imaging and cerebrospinal fluid (CSF) analysis 8 months after the surgery, the male Boxer’s outcome was considered excellent.

Emphasis has been placed on how to manage this disease through careful management practices including: proper handling, preventing crowding situation with animals, and transportation. Both the animals and the environment should be treated thoroughly to hinder the spread and control the fungal infection. This is especially important since humans can also contract this disease.

Fungicides applied specifically for downy mildew control may be unnecessary. Broad spectrum protectant fungicides such as chlorothalonil, mancozeb, and fixed copper are at least somewhat effective in protecting against downy mildew infection. Systemic fungicides are labeled for use against cucurbit downy mildew, but are recommended only after diagnosis of this disease has been confirmed. In the United States, the Environmental Protection Agency has approved oxathiapiprolin for use against downy mildew.

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.

Treatment is in the form of supportive care. If there is light-headedness, the victim should lie with feet partly elevated. If there is severe wheezing, then intramuscular epinephrine should be given, 0.5–1 ml at dilution of 1/1000 (standard medical emergency kit). An intravenous antihistamine like diphenhydramine should be given if needed.

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.

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.

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.

Currently, no treatment is available.

Good husbandry measures, such as high water quality, low stocking density, and no mixing of batches, help to reduce disease incidence. To eradicate the disease, very strict protocol with regards to movement, water sources and stock replacement must be in place – and still it is difficult to achieve and comes at a high economic cost.

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.

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.

Chelation therapy for acute inorganic mercury poisoning can be done with DMSA, 2,3-dimercapto-1-propanesulfonic acid (DMPS), -penicillamine (DPCN), or dimercaprol (BAL). Only DMSA is FDA-approved for use in children for treating mercury poisoning. However, several studies found no clear clinical benefit from DMSA treatment for poisoning due to mercury vapor. No chelator for methylmercury or ethylmercury is approved by the FDA; DMSA is the most frequently used for severe methylmercury poisoning, as it is given orally, has fewer side-effects, and has been found to be superior to BAL, DPCN, and DMPS. α-Lipoic acid (ALA) has been shown to be protective against acute mercury poisoning in several mammalian species when it is given soon after exposure; correct dosage is required, as inappropriate dosages increase toxicity. Although it has been hypothesized that frequent low dosages of ALA may have potential as a mercury chelator, studies in rats have been contradictory. Glutathione and "N"-acetylcysteine (NAC) are recommended by some physicians, but have been shown to increase mercury concentrations in the kidneys and the brain.

Chelation therapy can be hazardous if administered incorrectly. In August 2005, an incorrect form of EDTA (edetate disodium) used for chelation therapy resulted in hypocalcemia, causing cardiac arrest that killed a five-year-old autistic boy.

Initially, infected fish are known to "flash", or sporadically dart from one end of an aquarium to another, scratching against objects in order to relieve their discomfort. They will also "clamp" their fins very close to their body, and exhibit lethargy. If untreated, a 'dusting' of particles (which are in fact the parasites) will be seen all over the infected fish, ranging in color from brown to gold to green. In the most advanced stages, fish will have difficulty respiring, will often refuse food, and will eventually die of hypoxia due to necrosis of their gill tissue.

One way to control downy mildew is to eliminate moisture and humidity around the impacted plants. Watering from below, such as with a drip system, and improve air circulation through selective pruning. In enclosed environments, like in the house or in a greenhouse, reducing the humidity will help as well.

In cases of suspected copper poisoning, penicillamine is the drug of choice, and dimercaprol, a heavy metal chelating agent, is often administered. Vinegar is not recommended to be given, as it assists in solubilizing insoluble copper salts. The inflammatory symptoms are to be treated on general principles, as are the nervous ones.

There is some evidence that alpha-lipoic acid (ALA) may work as a milder chelator of tissue-bound copper. Alpha lipoic acid is also being researched for chelating other heavy metals, such as mercury.

There are a few controls for beech bark disease. One important management strategy is prohibiting the movement of nursery stock or other materials that may harbor the beech scale insect. Insecticides, generally not applied under forest conditions, are primarily used on high-value ornamental trees. The use of other organisms as controls is also a possibility. The ladybird beetle is a beetle that preys on the beech scale insect. A fungus that parasitizes the "Neonectria" fungus could also be employed. The problem with using these organisms to control beech bark disease is that their impact on the disease has not been evaluated extensively. In a forest setting, controlling the beech bark disease is too costly. Timely salvage cutting can reduce economic losses of beech in a forest. In stands where beech bark disease is established, silvicultural best practice is to retain large overstory trees which show visual resistance (no scale, cankers or fungus), remove heavily infested/dying trees and then treat sprouts from infested trees with herbicides. The residual, resistant parent trees are future sources of resistant seed/sprouts. Resistance to beech bark disease in a stand may be 1%-5% of trees or more, with significant regional variation. A study of 35 sites in three Canadian provinces found resistance rates ranging from 2.2%-5.7%.