There is an old saying that goes: "An ounce of prevention is worth a pound of cure" and this holds very true for diseases and parasites in a marine aquarium. It is far better to prevent the introduction of a problem in the first place than to have to get rid of it once it is already in the tank.
There really is only one effective method of preventing the introduction of disease or parasites into a display tank and that is with quarantine.
Quarantine has long been recognised as the most appropriate method of preventing (or at least limiting) the introduction of exotic or otherwise unwanted organisms from entering a controlled environment. It is a scientific protocol and countries use quarantine to prevent pests and disease from entering a country or areas within the country.
A quarantine tank won't actually prevent the introduction of diseases or parasites into the display tank, but significantly reduces the chances of it and so can be considered effective.
The main idea behind a quarantine tank is to provide sufficient time for any parasites that may have been present on the fish at the time of introduction to have reproduced so that their presence becomes obvious and then appropriate treatment can be commenced. Six weeks should allow for enough time for detection of most problems but if the fish can be kept here for longer, the margin of safety is increased.
Many hobbyists and even some books recommend freshwater dips as a method of preventing the introduction of disease and parasites into the display tank. New fish are given a freshwater dip before being placed into the display tank to eliminate parasites. Unfortunately, this demonstrates a lack of understanding of most of the parasites that infect marine fish.
While freshwater dips are helpful for the treatment of some conditions, such as Amyloodinium and Turbellaria, they are ineffective for common problems such as marine "Ich" and Brooklynella. This means the unaffected parasites can still be introduced into the display tank.
Colorni found that freshwater dips are not effective for Cryptocaryon. Infected fish still had attached trophonts even after being in freshwater for 18 hours. The trophonts were still viable and completed their normal life cycle after the fish were returned to normal salinity. The dip may remove some parasites, but if it doesn't remove all of them, it is of little value as the fish will become infected again.
Freshwater dips work very well for for removing Amyloodinium parasites, but there is still the possibility of some trophonts staying attached and being able to complete their life cycle. Freshwater does not kill the parasites. So, while freshwater dips can provide some relief to the fish, they should not be used as the sole form of treatment for Amyloodinium.
There are various multicellular parasites, such as flatworms (including turbellaria and monogenea) and crustaceans (including isopods and copepods) for which freshwater baths are effective. It is important to note that for the flatworms, there may still be some flatworms in the tank and multiple treatments may be necessary.
Based on the above, there is little value in giving all new fish a freshwater bath before placing them in the main tank, as it won't stop Cryptocaryon or Brooklynella and it unlikely to stop Amyloodinium.
Note that it is also unwise to freshwater dip new fish before putting them in quarantine. As a freshwater dip may reduce some parasites rather than eliminate them, a freshwater dip may simply prolong the onset of signs to the point that the fish are already in the display tank before you know they are infected. Placing the fish straight into the quarantine tank and leaving them there for at least 6 weeks greatly improves the chances of any infections becoming obvious.
Quarantine with UV Sterilisation
Some hobbyists believe that a quarantine tank with a UV steriliser provides more protection that the quarantine tank on its own. Unfortunately, due to the lack of full control of parasites by UV sterilisation (see below) the combination may make matters worse by reducing the number of parasites present but not eliminating them. This may only mask a problem which will become evident only when the fish is moved to the display tank.
In the context of this page, disease and parasite control refers to minimising the effects of disease or parasites already in the display tank.
Unfortunately, there are no fully effective methods although some of the methods below may be of value for some ailments
The methods listed below are often seen by hobbyists as effective ways to control parasites that may be present in the display tank. While some of them may assist and even prevent deaths, they are not effective for all parasites and some are not effective at all.
Ultra Violet radiation is lethal to living tissue and this principle is used with a UV steriliser. Tank water is circulated through the unit where it is exposed to UV radiation. If the amount of UV radiation and contact time are appropriate, everything within the water will be killed.
For a UV steriliser to be effective at killing everything that passes through it the flow rate must be matched with the size UV tube to ensure appropriate irradiation rates and contact times. This is first area where the use of UV sterilisation breaks down. If the unit is too small and/or the flow rate through it is too high, many organisms can pass through the unit unharmed.
The second problem with UV sterilisation is that only organisms that pass through the unit will be killed. Some parasites, such as Brooklynella, transfer directly from fish to fish and spend little or no time in the water column and as such won't pass through the UV steriliser. UV sterilisation will be ineffective for these types of parasites.
Parasites such as Cryptocaryon and Amyloodinium have life cycles with multiple phases and one or more phases are spent in the water column. It is these phases that are candidates for UV sterilisation. Unfortunately, these phases are very short and while some parasites may pass through the steriliser some will not and will be able to complete their life cycle and reproduce, maintaining at least some presence in the tank.
Gratzek et al  showed that for Ichthyophthirius multifiliis (a freshwater parasite with a life cycle very similar to Cryptocaryon), UV sterilisation was very effective for preventing the spread of parasites from one aquarium to another in a multiaquaria system, but did not prevent the infection of fish within a tank where I multifiliis already existed. In the absence of similar studies on Cryptocaryon, it can be assumed that the results with the marine parasite will be similar.
At best, a UV steriliser can reduce the number of parasites to a level that will not be life threatening to the inhabitants. At worst, they will do nothing, either because of inappropriate size/flow rate or simply because they are not effective for some parasites.
Ozone for disease control works on much the same principle as UV sterilisation. Ozone is highly reactive and oxidises living material. As with a UV steriliser, the flow rate of the ozone and the flow rate through the chamber need to be tuned to ensure the death of organisms that pass through it.
Ozone has the same limitations as UV sterilisation and is only effective against organisms that pass through the unit.
Many hobbyist believe that because cleaner wrasses and cleaner shrimp feed on parasites in the wild, they are effective for parasite control in the aquarium. Unfortunately, the parasites that are common in aquaria are not common in the wild. The life cycles of these parasites are such that in the confines of an aquarium, their reproduction rate and method of infection is far more effective and fish are infected with much higher numbers of parasites than they would in the wild.
The natural diet of Labroides dimidiatus (common cleaner wrasse) is almost entirely the larvae of gnathiid isopods. These are multicellular parasites that attach to the skin and gills of (larger) fish. Mucus and bits of skin have also been found in their gut. It is doubtful that these fish would show much interest in "Ich" trophonts and even less likely they would be interested in the smaller trophonts of Amyloodinium and Brooklynella.
When the Cryptocaryon trophonts attach to the fish, they burrow deeply into the skin of the fish and are covered over by the mucus of the fish. So much so, that they are impervious to chemicals such as copper and also to freshwater (even after 18 hours). The only potentially viable treatment option against the trophonts to date, involves initial treatment with hypersaline water to cause the loss of the mucus layer so that subsequent treatments can reach the parasites. Given this, it is unlikely that either cleaner wrasse or cleaner shrimp would be able to remove the parasites.
There is also a lot of anecdotal evidence from people that have lost fish to "Ich" in tanks where either or both cleaner wrasse and cleaner shrimp were present. Granted, there is also anecdotal evidence where fish recovered from "Ich" when either or both were present, but the following questions remain from that evidence: Was it really "Ich"? Did the "Ich" really go away? Were the cleaners at all responsible for it going away?
It should be noted that some aquarists believe they have seen cleaner wrasses picking Cryptocaryon trophonts off infected fish so it may be possible they will take some parasites. Unless the infected fish are significantly larger than the cleaner, it is very unlikely that the cleaner wrasse would be able to remove parasites from the gills where they do the most damage. It is also unlikely that the cleaner wrasse would remove all the parasites so some will be able to complete feeding, drop off the fish and reproduce.
- (http://www.int-res.com/articles/dao/1/d001p019.pdf): Colorni, A., Aspects of the biology of Cryptocaryon irritans, and hyposalinity as a control measure in cultured gilt-head sea bream Sparus aurata, Diseases of Aquatic Organism, 1, (1985), 19-22.
- (http://links.jstor.org/sici?sici=0022-3395%28198702%2973%3A1%3C85%3AASMOPT%3E2.0.CO%3B2-Y): Bower, C.E., Turner, D.T., and Biever, R.C., A standardized method of propagating the marine fish parasite, Amyloodinium ocellatum, The Journal of Parasitology, 73(1), (1987), 85-88.
- (http://www.blackwell-synergy.com/doi/pdf/10.1111/j.1365-2761.1983.tb00062.x): Gratzek, J.B., Gilbert, J.P., Lohr, A.L., Shotts, E.B., and Brown, J., Ultraviolet light control of Ichtyophthirius multifiliis Fouqet in a closed fish culture recirculation system, Journal of Fish Diseases, 6(2), (1983), 145–153.