The Exact Koi Quarantine Protocol I Use: A Proven 14-Day System for Healthy, Parasite-Free Fish

Quarantining new koi is the single most important step in preventing parasites, bacterial infections, and disease outbreaks in your pond.
As a 30-year aquaculturist who has handled thousands of fish—from domestic stock to high-end Japanese imports—this is the exact, real-world protocol I follow every time new koi arrive.

If you want a quarantine process that actually works, protects your existing koi, and eliminates the most common problems before they reach your pond, this is it.

Why Proper Quarantine Matters

Most koi arrive stressed, immunocompromised, and carrying some level of parasites or bacteria—even from reputable breeders. A proper quarantine protocol gives them time to stabilize, shed parasites, and recover before being exposed to your main pond.

Poor or rushed quarantine is the leading cause of:

Fluke infestations

Anchor worm and fish lice outbreaks

Ulcers and bacterial infections

Sudden spring parasite blooms

Massive losses after new fish introductions

This is why a structured program is critical—and why hobbyists who skip quarantine often end up with preventable health issues.

Days 1–2: Arrival and Salt Stabilization (5 ppt)

When fish arrive, I immediately place them into the quarantine system and raise salinity to 5 ppt, which is 5 pounds of salt per 100 gallons.

This step:

Reduces osmotic stress

Helps stabilize electrolyte balance

Suppresses early parasite activity

Supports slime coat repair

The fish stay in 5 ppt salt for 48 hours with no other treatments added.

This stabilization period is crucial. It allows the immune system to reboot before starting any medications.

Day 3: Reduce Salt to 1 ppt and Treat With Purple Magic

After 48 hours, I perform a water exchange to bring the salinity down to 1 ppt or less.
Once the salt is reduced, I administer a full treatment of Purple Magic.

Purple Magic helps control bacterial load, target early ulcer development, and prevent common infections from gaining traction during the transition period.

Days 4–6: First Prazi Power Treatment (Flukes)

Flukes are the number one parasite found on new koi, and you should assume every new fish has them unless proven otherwise.

On Day 4, I begin Prazi Power at 1.5 g per 100 gallons, allowing it to remain in the system for three full days with no water changes.

This first cycle wipes out adult flukes and most juveniles.

Day 7: Flush the System and Start Anchor Armor

On Day 7, I flush the entire quarantine system and refill with clean, dechlorinated water. Immediately after refilling, I treat with Anchor Armor.

Anchor Armor targets:

Anchor worm

Fish lice

Crustacean parasites that Prazi does not handle

I maintain Anchor Armor in the system for three days.

This combination—Prazi Power followed by Anchor Armor—covers the full spectrum of external parasites commonly introduced with new koi.

Day 10: Optional Second Prazi Power Treatment (Highly Recommended for Japanese Imports)

This step is technically optional, but I personally do it for every Japanese koi and any high-value fish.

On Day 10, I administer a second Prazi Power treatment at 1.5 g per 100 gallons and allow it to sit for another three days.

Why this step matters:

Fluke eggs survive chemicals

A second round targets new hatch-outs

It dramatically reduces the chance of flukes entering your pond

Skipping this step is one of the most common reasons hobbyists experience fluke outbreaks shortly after adding new fish.

Days 11–13: Observation and Behavior Monitoring

Once treatments are complete, I shift into a monitoring phase.
During these days, I watch closely for any signs of:

Flashing

Gasping at the surface

Clamped fins

Lethargy

Loss of appetite

Isolation from the group

By this stage, fish should be eating, active, and showing stable behavior.
Any issues that present now should be handled before the fish reach the pond.

Day 14: Acclimate and Introduce to the Pond

If fish look healthy, stable, and behaviorally normal by Day 14, they are ready to be acclimated and moved into the main pond.

A koi that completes this process enters your system:

Parasite free

Stabilized

Eating well

Adjusted to captive conditions

No longer stressed from transport

This is how you protect your pond and maintain long-term health and stability.

Written by Jason Michael, a 30-year aquaculture professional with experience in commercial koi farming and fish health management.