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Quarantine a New Fish: The Fundamentals

A simple quarantine routine for watching a new fish before it joins the main tank.

Category
Getting Started
Published
Jul 20, 2026

Quick answer

Give the fish a quiet space, stable water, and a few weeks of prophylactic medication, and careful observation before being allowed into show tanks.

Practical steps

  1. Set up a separate tank or container with stable, fish-safe water.
  2. Watch feeding, breathing, swimming, and waste for several weeks.
  3. Keep tools, nets, and water containers separate from the main tank.
  4. Move the fish only after it has been stable long enough to look settled.
  5. Medicate the fish prophylactically via multiple rounds of medication, eliminating parasites and eggs.

Quarantine is by far the best act of prevention that a hobbyist can engage in in order to not only protect their investment but also to safeguard the aquascapes they have made and the health of the livestock they already enjoy. The key to quarantine is to remember that your chosing to confront disease and sickness before it can put at risk the animals and plants that you already have worked hard to enjoy and invested in. There are some fundamentals that you must understand as you quarantine. The first is that your often going directly against pathogens that if left alive can do far more damage to your investment in fish and aquascapes should they get access to those. Thus its better to fight that battle on your terms and in a location of your own choosing. Thus the quarantine tank or the hospital tank will be what is used. Quarantine is an active process of cleansing the fish. Remember that pathogens have protections as well. Some are only vulnerable to medicines during a particular portion of their life cycle and others have egg forms that can’t be poisoned until the parasites themselves emerge from their eggs. Thus this isn’t a fast process, its a slow one when done correctly. Here are some of the fundamentals of quarantine:

1.) Filtration is Still Fundamental:

  • Filtration is a challenge in quarantine systems. What makes it challenging is that quarantine filtration must be capable of working at top efficiency at a moments notice even if it hasn’t seen fish in months. Additionally some medications can kill the very bacteria that we depend upon for keeping the water clean. When this occurs we are left with a very difficult decision of how to continue treatment and also manage the pollution of the water. For this reason hobbyists tend to be very selective on what medications that we use. Sponges are a favorite for most quarantine systems. Sponges by in large are interchangeable this means that when fish are introduced to the quarantine tank, sponges that have already been used can be squeezed out and transferred from a clean tank into the quarantine tank. Those sponges having already been seeded with active colonies of bacteria are already bioactive and ready to convert ammonia into nitrate. The sponge previously used can now be desiccated and cleansed for future use. Of particular use in a quarantine tank are sponges that contain pockets for bags of filtration. The substrate bags can be filled with peat if the water needs to be softened. They can also be filled with activated carbon should the need arise to rapidly take out medication from the water. This can be a life saving addition to the arsenal especially when dealing with smaller tetras that can be particularly sensitive to certain medications. It can be the difference between life and death and can allow the hobbyist to rapidly remove any medication that they find is not compatible with the particular fish that they are treating in quarantine.

2.) The Problem of Volume.

  • Hobbyists choose to use smaller volumes tanks in order to keep costs low. Simply put medications can be expensive and the cost of dosing a show tank can be more then ten times that of dosing a single ten gallon tank. Thus if the quarantine tank is a temporary holding facility anyway, it makes sense and is cost effective to use less medicine. There is also the additional benefit that medicines can also come prepackaged per ten gallon packets. Thus its easy to use prepackaged medicines that are aimed at that volume of water. You simply open the package and pour it in. Finally medications also require you to eliminate water between usage. This usually falls between 10 and 30% depending on the medication. Using a 10 gallon tank makes the calculation easy as every gallon is 10%.

3.) Tools must be confined to Quarantine:

  • This is often the most missed part of quarantine when you are dealing with diseases that are water born. Thus siphons, nets, and any tool that goes into the water including your hands and arms must be cleaned before it comes into contact with any other tank. Some times its just not practical to sterilize implements using traditional methods. When we lack the ability to clean these tools quickly and thoroughly enough the only practical solution is what is known as desiccation. Desiccation is the practice of allowing anything that comes into contact with the water to thoroughly dry itself out. The overwhelming majority of fish borne illnesses are designed for life in the water. Thus desiccation is effective at killing these pathogens making their dried up corpses an inert mound of matter incapable of harming anything else. In order to desiccate an object, time is required for the water to evaporate away. Thus having a set of tools that can only be used in a hospital tank and is dedicated to that particular tank is the wisest course of deliberate action that confines pathogens to tanks that contain sick fish and prevents cross contamination.

4.) What to look for:

  • There are several markers that one must consider when observing fish in quarantine. By far the best thing to look for is fish poop. Fish poop should be long and brown. The poop of a healthy fish should not be grey, whispy, or stringy. Poop that is grey, whispy, stringy is often the characteristic of internal parasites that should be treated. Are the fish gasping for air? This can be a sign of gill flukes. This too should be treated while in the hospital tank. How is the fish’s appetite? Is it eating voraciously, gorging itself on what is provided. If so this is a good sign. Does it bite at food but it doesn’t actually swallow it? This is a sign of an infection and needs to be treated. Do you see white spots on the skin or the eyes of the fish, this is a sign of a disease that absolutely must be treated before coming into contact with any other organisms. Is the fish’s belly caved in? Again this can be a sign of internal parasites and you need to treat this before the fish gains access to your show tanks. All of these signs will be treated with multiple rounds of medication. One round to get the adults followed by a week of rest and then a second round to kill the eggs that hatch one week later before they can become adults and deposit eggs into the hosts themselves.

5.) Use this time as an Opportunity:

  • Quarantine is a time which requires your attention to detail. Often times fish will exhibit subtle and not so subtle clues that gives hints to their personalities, wants, and needs. Two examples of this when I first acquired Tetradon schodenti, also known as the Congo Spotted Puffer, while in quarantine I began feeding the puffers live feeder shrimp as the literature at the time stated that they fed exclusively on invertebrates. The literature wasn’t exactly wrong at the time, they did eagerly go after shrimp. However it wasn’t exactly right either as I soon found out as I was treated to this fish trying its very best to lunge at the shrimp and missing them horribly. It was then that I observed something else. While they missed the shrimp more times then they even came close, what they were succeeding in tearing up with their sharp, strong teeth were the plants that would not evade their lunges like the shrimp did. I learned right away that this fish would tear apart the plants in its tank as it clumsily went after the more agile shrimp. Later on I also learned what foods they had evolved to capture and kill. These foods were of course snails. As I watched two Schodenti puffers, recognize a snail in the next tank over and try their very best to push against the glass to get that snail. Observing behavior can tell you a lot about how that fish will function.
  • You can also tell if the particular fish are nocturnal or diurnal. Observation of when the fish moves and when it doesn’t move is of particular interest when you need to determine what is normal and abnormal in an animal. This is especially true when your keeping animals that don’t have a lot of documentation to accompany them due to their being newly discovered to the hobby.
  • How aggressive are they? This is something you will begin to see as the fish settles down in the quarantine tank. Interspecies aggression will begin to develop as the fish try to claims the territory around them. Those that do while in the quarantine tank gives you hints as to what will be required when you put them into a show tank. Specifically those that immediately try to claim territory such as African cichlids, really need to have the show tank disrupted and the scape changed in order to allow them to claim territory when depositing the fish into the show tank when quarantine is done.
  • Are the fish adjusting to the food that you want them to consume. This is a big one. Many times especially with wild fish, the food your feeding isn’t what they recognize as food. You want to ensure that before they enter your show tanks that they recognize what food is and that you bring food for them. This way they associate you with food and compete for it immediately upon placement into the water.

6.) The medications that Should be in your cabinet:

  • This is the most important step of quarantine. When you quarantine there are two approaches. The first approach is to observe and use medication only when signs of sickness emerge. The author of this page is not in favor of this approach. The approach that I use assumes that illness is hiding and the fish are already infected with pathogens that will become a headache later on. To this end, I would recommend that you follow suit and treat for the illness I assume to be there in stages. Now if you choose to utilize this approach the next question will be then what do we use to treat the illnesses the fish may have been exposed to but are not yet showing evidence of. What I will recommend that you use was primarily proffered for consideration first by Mr. Cory McElroy of Aquarium Co op. I will summarize the medications recommended below. It is important that the medications be followed per the advice of the manufacturer as failure to do so develops strains of pathogens that build resistance to the medications. Now the medications that we will use is four fold. The first three were recommended by the Aquarium Co op the last one comes from years of experience dealing with livebearers. I have only found the need to administer the fourth to livebearers. The answer to this is four fold, and for 90% of the diseases that we routinely encounter in the hobby these four medications are sufficient:
  • General Cure: General cure by API is the combination of the antibiotic Metronidazole and Praziquantel in one medication. General cure does not seem to target the bacteria found in filters thus it is also considered filter safe by many aquarists. General cure is for internal infections and external parasitic infections so things like hexamita and hole in the head disease is addressed by the Metronidazole while parasites such as flukes, tape worms, and flatworms are addressed by Praziquantel.
  • Erythromycin: Erythromycin is a general antibiotic used to treat gram positive bacterial infections such as fin rot and gill diseases. It can also be very useful in helping control epistylis due to the fact that the organism that causes epistylis eats live bacteria that his anti biotic helps eliminate. It is considered a gentle antibiotic and doesn’t seem to target filter bacteria.
  • IchX for Freshwater. IchX for freshwater is the combination of two medications. These medications are formalin and malachite green. These medications in combination target free swimming parasitic stages such as what is found in the infamous fish disease known as ich. It is also effective at controlling another disease that looks very similar to Ich in Epistylis.
  • Levamisole: Levamisole is a medication that I always give to livebearers that come through my fish room as a part of their quarantine. It is effective in the treatment of camallanus worms. The way that it works is unique. While other medications seek to kill the parasite outright, camallanus worms are internal worms that are very difficult to eliminate. The way this medication works is its a paralytic. It paralyzes the worms that are inside of the fish. This allows the fish to excrete the worms and allows the fish keeper to pick them up when vacuuming the bottom of their tanks thereby eliminating them from the system.

7.) The Stages of Dosage: It is important to note that one should always follow the instructions of the manufacturer. This includes all aspects of medicating the water including doing the routine water changes in exactly the same manner as described by the manufacturer. I also recommend medicating one more time in each sequence. This additional medication regiment helps ensure that they pathogens that you want to eliminate are in fact eliminated. Finally after one week, it is highly recommended that you medicate the fish again starting on the eighth day and continuing as the treatment schedule as the manufacturer demands and extending it one more day. The reason for this is simple, the first time you medicated you eliminated the adults. The eggs that they laid inside of the fish may not have been eliminated. The second round of medication rounds these organisms up before they have a chance to reproduce themselves. Following this regiment allows for the elimination of most pathogens before they can become a headache in your carefully scaped and invested in show tanks.

Sources and review

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