Several factors must be considered when deciding whether or not to quarantine an animal before introducing it into your aquarium, or when providing medication. The use of a quarantine aquarium requires the animal to adapt to an additional change in environment and water conditions. Such changes are stressful in and of themselves and may make recovery from illness more difficult.

Many hobbyists keep newly acquired animals separated from their collection for a three to four week period to assess the animals' health and to be sure that they will not introduce disease or parasites into the main aquarium. In general, quarantine aquariums should be sparsely furnished so they can be easily cleaned when new animals are introduced, and so the confined creature is more readily observed. However, you must be sure to meet the quarantined animal's environmental needs and to provide it with shelter, if necessary. For this reason, animals that require complex, well planted exhibits are more difficult to quarantine than are less sensitive species.

It is vital that the quarantine aquarium's physical parameters, such as temperature, pH, and specific gravity be very close to those that the animal will experience once it is introduced into the main aquarium. One exception to this rule might be in the case of salinity when dealing with marine animals. While most marine fish can tolerate a slightly lower than usual salinity, such as 1.018, most of their parasites cannot. Especially when keeping wild caught marine species, therefore, you might consider quarantining the animals at this lower salinity.

The quarantine aquarium must, of course, be kept extremely clean. Therefore, you should employ an effective but easily maintained filtration system. Since aesthetics are not your main concern here, a simple box filter placed within the aquarium may suffice. Be sure that the biological capacity of the filter is maintained. To do this, the beneficial aerobic bacteria in the filter must be provided with a food source. During periods when the quarantine aquarium is empty, be sure to add commercial preparations that provide food for the beneficial bacteria, or introduce commercially available aerobic bacteria before adding fish to the tank.

It is sometimes possible to treat an ailing fish within the main aquarium. This is especially possible if the animal is the aquarium's sole inhabitant, or if its tank mates will likely be affected by the disease as well.

Often, however, it is advisable to isolate a sick fish before trying to cure an illness with medication. Isolation will often be necessary when you are medicating fish housed in aquariums that contain invertebrates as well. Copper is the most common ingredient in medications designed to kill fish parasites. Most aquarium invertebrates cannot, however, tolerate even the slightest bit of copper in the water, so you will need to remove either them or the fish that is being treated before using such medications.

Certain medications will kill the beneficial aerobic bacteria living in your filtration system. To avoid a crash of your main tank's system, ill fish should be removed from the tank and treated separately if these medications are required. Of course, bear in mind that the quarantine aquarium's beneficial bacteria will also be killed off, so be sure to keep an eye on water quality.

Another factor to consider is that certain filtration materials, most especially activated carbon, will effectively remove medications from aquarium water, thereby negating their effect upon the sick fish. Read the directions carefully to determine whether or not you should remove activated carbon and other such materials from the filter before using the medication in question.