Quarantine: Disease, Parasite & Pest Prevention in Reef Tanks

New England Aquaculture
Mar 10
3 min read

Updated: Mar 14

System Options, Factors to Consider & Quarantine for Coral

An ounce of prevention is worth a pound of treatment—this saying holds true for reef tanks. Just like any living organism, fish and coral are susceptible to diseases, bacteria, parasites, and predators that can wreak havoc in a tank. To prevent introducing these threats, a proper quarantine protocol is essential. While it may sound daunting, the process is fairly simple and can save you from major losses in the long run.

System Options

To establish an effective quarantine, start by considering the space requirements of the species in question. Small fish like Chromis or Gobies can be quarantined together in a standard twenty-gallon long or thirty-gallon tank. However, larger, more territorial fish should be quarantined individually to avoid stress or aggression.

Once the quarantine tank is selected, fill it with clean saltwater and maintain a suitable temperature between 78-80 degrees Fahrenheit. This range enhances metabolic rates and improves the effectiveness of treatment. Filtration should be set up based on the level of treatment required.

Observation Quarantine: A simple trickle or hang-on-back filter with carbon and floss is sufficient.
Medication Quarantine: Carbon should be avoided, but filter floss remains useful.
Frequent Water Changes: In cases requiring frequent water changes, an air-pump-driven sponge filter may be the best option.

For optimal results, multiple quarantine systems are recommended. Careful observation may be sufficient for some fish, while others require proactive treatment for known parasites or worms.

Factors to Consider in Quarantine

The length of quarantine varies based on treatment instructions and additional factors:

Source of the Fish – If purchasing from a trusted local fish store where you can observe the fish beforehand, a short quarantine of a few days may suffice. However, fish from unknown or newly arrived sources may require extended observation and treatment.
Current Diet – If the fish is already eating a suitable food, quarantine may be shorter. If transitioning to a new diet, the process may take much longer.
Expert Consultation – Research, along with advice from experienced aquarists or your local fish store, will help determine the appropriate quarantine protocol.

Quarantining Coral

While fish require meticulous quarantine procedures to prevent diseases and parasites, coral is more resilient to these threats. However, corals are still at risk from pests such as flatworms, anemones, and polychaete worms. To manage these issues, corals should be quarantined in a separate system where copper-based medications should never be used.

Quarantine Setup – A simple container or large bowl with clean saltwater is sufficient.
Treatment Options:
- Antibiotic Dips – Various commercial coral dips are available to treat bacterial and fungal infections.
- Anemone Removal – Pests like Majano and Aiptasia anemones can be treated with targeted solutions.
- Worm Extraction – Traps or baiting techniques can help remove unwanted worms from coral frags.
- Freshwater & Iodine Dips – Tissue recession and flatworms can be addressed through these methods.

Corals that endure long transit times benefit significantly from proper dipping, as the buildup of mucus and waste increases their susceptibility to infection. Ensuring corals are properly acclimated and quarantined before introducing them to the main reef tank reduces risks and enhances the health of the system.

Why Quarantine Matters

A well-implemented quarantine protocol minimizes avoidable losses, promotes long-term health, and ensures the stability of your reef tank. By carefully observing, treating, and acclimating new additions, you prevent costly mistakes—such as a five-dollar damselfish introducing a fungus that wipes out a prized ten-year-old angelfish.

Get Expert Guidance with New England Aquaculture

Need help setting up a proper quarantine system? New England Aquaculture offers Service and Consultation Plans to guide you in disease prevention, system design, and best practices. Contact us today to ensure the long-term success of your reef tank!