The Complete Koi Quarantine Guide: Everything You Need to Know

By KoiQuanta Editorial Team|Updated Mar 2026

Hobbyists who follow a structured quarantine protocol reduce new-fish-related losses by over 85% compared to unprotected pond introductions. That's not a marginal improvement: it's the difference between a healthy established pond and repeated cycles of disease introduction, treatment, and loss.

This guide covers the complete koi quarantine protocol from scratch. It was developed with professional koi health consultants and backed by vet-validated protocols, the same framework embedded in KoiQuanta's quarantine workflow. Whether you're setting up your first quarantine system or tightening an existing one, this is the full picture.

TL;DR

You can buy from the best dealer in the country and still introduce Koi Herpesvirus, Cyprinid Herpesvirus 2, or sub-clinical bacterial infections into a healthy established population.
For larger fish, aim for a minimum of 300–500 gallons.
A good rule: each inch of koi gets 10 gallons of quarantine water minimum during the active screening period.
An uncycled quarantine tank will produce an ammonia spike within 24–48 hours of adding fish, and an ammonia-stressed fish is not in condition to mount an immune response.
Run at minimum one air stone per 100 gallons of quarantine volume.
A koi carrying Ich at 10°C may not show spots for weeks.
At 22°C, Ich typically becomes visible within 5–7 days.

Why Quarantine Is Non-Negotiable

Every new koi you add to your pond is a potential disease vector. You can buy from the best dealer in the country and still introduce Koi Herpesvirus, Cyprinid Herpesvirus 2, or sub-clinical bacterial infections into a healthy established population.

The problem isn't that dealers are selling sick fish. The problem is that koi can carry pathogens subclinically, appearing healthy while actively shedding infectious agents. Transport stress suppresses their immune system and allows previously controlled infections to become active. Your established fish have no immunity to pathogens they've never been exposed to.

Quarantine creates the buffer that protects your pond. It's not just about watching for obvious illness: it's about creating the controlled conditions that push subclinical infections into visibility before they reach your display pond.

The Quarantine System: What You Need

Tank Size

For most residential koi up to 18 inches, a 200–300 gallon quarantine tank is workable. For larger fish, aim for a minimum of 300–500 gallons. The quarantine tank doesn't need to be decorative: a stock tank, IBC tote, or purpose-built rectangular fibreglass tank all work.

The fish should have enough water volume to avoid severe crowding stress. Crowding suppresses immunity and masks the disease screening you're trying to accomplish. A good rule: each inch of koi gets 10 gallons of quarantine water minimum during the active screening period.

Filtration

This is the single most critical setup element. Your quarantine tank needs biological filtration capable of processing the waste load of your incoming fish. An uncycled quarantine tank will produce an ammonia spike within 24–48 hours of adding fish, and an ammonia-stressed fish is not in condition to mount an immune response.

Options for fast filter establishment:

Run a sponge filter in your main pond for 2–4 weeks before you need it, then transfer to quarantine
Use commercially available nitrifying bacteria products (Nitrospira/Nitrosomonas seeded filters)
Add mature filter media from your established pond filtration

A properly cycled quarantine filter prevents the ammonia spikes that stress and kill new koi before disease even becomes a concern.

Aeration

Quarantine tanks are often under-aerated. More fish than usual in a smaller volume means higher oxygen demand. Run at minimum one air stone per 100 gallons of quarantine volume. Two or more air stones is better, especially in warmer water.

Heating

For disease screening purposes, a stable temperature between 20–24°C is ideal. This temperature range activates immune function and, importantly, encourages pathogens to complete their lifecycle and become visible. A koi carrying Ich at 10°C may not show spots for weeks. At 22°C, Ich typically becomes visible within 5–7 days.

A 300-watt submersible heater with a reliable thermostat is sufficient for most quarantine volumes.

Cover

Koi in quarantine are stressed and prone to jumping. Always cover the quarantine tank.

The 30-Day Quarantine Protocol

Thirty days is the minimum validated quarantine period for koi imported from overseas or from unknown sources. For koi from trusted domestic suppliers with known health status, 14 days is sometimes used, but 30 days gives you much higher confidence.

KoiQuanta's quarantine workflow automates the entire schedule below, sending you step-reminders at each stage and logging completion automatically.

Days 1–3: Arrival and Stabilisation

Add fish to the quarantine tank. Add salt at 0.1% (1 lb per 100 gallons) immediately: this reduces osmotic stress without being a full therapeutic dose. Don't add more salt yet.

Do not feed for the first 24 hours. Allow fish to stabilise in the new water before adding the stress of feeding.

Observe closely. Fish will be stressed from transport. Expect some flashing, sitting at the bottom, or surface hovering in the first 24 hours. This is normal transport stress, not necessarily disease.

Test water daily: Ammonia, nitrite, temperature. Act immediately if ammonia rises above 0.25 ppm.

Days 4–7: First Observation Window

Feed sparingly: no more than fish can consume in 2–3 minutes, once daily. Watch for:

Flashing or rubbing against surfaces (parasites)
Clamped fins, unusual colouration
Spots or lesions developing
Abnormal swimming behaviour

On day 5–6, raise salt to 0.3% (add salt to bring from 0.1% to 0.3%). This is your parasite-suppression concentration.

Test daily: Ammonia, nitrite. Test KH and pH on day 7.

Days 7–14: Active Disease Screening

This is the core observation window. By day 7, most common external parasites will be visible or actively affecting fish behaviour if present.

Perform a full physical examination, ideally a light scraping for microscope examination if you have the capability, or a careful visual inspection:

Check fins for damage, white spots, or fraying
Check body for ulcers, raised scales, or lesions
Check around the face and gills for swelling or unusual colouration

If you find any issue, begin the appropriate treatment before proceeding. Do not release fish to your main pond with any active health concern.

Continue: Salt at 0.3%, daily feeding, water quality tests every 2 days.

Days 14–21: Second Observation Window

Many pathogens have incubation periods of 7–14 days. The second observation window is designed to catch cases that weren't visible in the first two weeks.

Perform another physical examination on day 14–15. If you treated a parasite issue in weeks 1–2, assess treatment effectiveness now.

Maintain water quality. Continue daily feeding at normal rates if fish are active and healthy.

This is also the point where fish are typically comfortable enough in quarantine that you can assess their true appetite and behaviour: suppressed feeding in week three, when the fish should have recovered from transport stress, is a meaningful clinical sign.

Days 21–28: Final Observation

Continue observation. If all has been clear through weeks 1–3 and fish are feeding and behaving normally, the 30-day protocol is nearly complete.

Perform a final physical examination at day 28. Look for any late-presenting issues.

Begin the salt reduction process. Reduce salt concentration gradually through water changes over days 25–30. Removing salt too abruptly is stressful; gradual reduction over 5–7 days is preferred.

Day 30: Clearance Assessment

Before releasing to your main pond, confirm:

All water quality parameters have been stable and within safe range
No disease signs have been present for at least 14 days
Fish are feeding actively
Physical appearance is healthy (no lesions, spots, fin damage)
Salt has been reduced to match main pond concentration

In KoiQuanta, the clearance checklist ensures every criterion is met before the fish are recorded as cleared. The clearance date, conditions, and digital signature are all logged and available for compliance records if you're a dealer.

Disease Screening During Quarantine

What to Screen For

External parasites: White spot (Ich), Costia, Trichodina, anchor worm, fish lice. Visual inspection identifies most of these. Mild flashing can be normal; persistent flashing with visible spots or lesions requires treatment.

Bacterial infections: Ulcers, red patches, swollen areas. Any active ulcer during quarantine requires treatment before clearance.

KHV (Koi Herpesvirus): The most feared koi disease. KHV is temperature-sensitive: it becomes active and detectable at 18–26°C. This is another reason why maintaining quarantine temperature in this range matters. Signs include gill necrosis, excessive mucus, and rapid decline. If you suspect KHV, contact an aquatic vet immediately. KHV is notifiable in many countries.

Gill health: Look for laboured breathing, surface hovering, or rapid operculum movement. Gill flukes (Dactylogyrus) are a common quarantine find and treatable with praziquantel.

Salt Treatment During Quarantine

Salt at 0.3% throughout the 30-day protocol does multiple things:

Reduces osmotic stress on fish with compromised barriers
Has mild antiparasitic properties against some external parasites
Supports recovery from transport stress

The salt treatment during quarantine protocol in KoiQuanta manages your salt concentration throughout the 30 days, accounting for water changes and flagging when concentration drops below the therapeutic threshold.

Quarantine for Dealers: Compliance and Documentation

For koi dealers and importers, quarantine isn't just a fish health practice: it's a compliance requirement. USDA APHIS and most state departments require dealers to maintain documented quarantine records for imported fish.

KoiQuanta generates audit-ready quarantine documentation as a side effect of executing the normal protocol. Every water test, treatment, observation, and clearance decision is timestamped and exportable in formats compatible with USDA audit requirements.

The 30-day koi quarantine program in KoiQuanta is the execution tool. The new koi quarantine protocol documentation template gives you the paper framework that compliance records build on.

Common Quarantine Mistakes

Too short a quarantine period. Two weeks is not enough. Fourteen days misses pathogens with 7–14 day incubation periods. Thirty days is the validated minimum for meaningful disease screening.

An uncycled filter. Ammonia poisoning during quarantine defeats the entire purpose. Establish your filter before fish arrive.

Temperature too cold. Quarantining at 10–15°C means pathogens won't show themselves, and fish won't mount a proper immune response. 20–24°C is the right range.

Skipping physical examinations. You can't find what you don't look for. Schedule and perform the physical checks at the week marks.

Releasing fish too early when they "look fine." Looking fine is not a 30-day structured quarantine. Complete the protocol.

FAQ: Complete Koi Quarantine Protocol

What is the complete koi quarantine protocol?

The complete koi quarantine protocol is a 30-day structured program involving: immediate salt treatment at 0.1% rising to 0.3%, daily water quality monitoring, scheduled physical examinations at days 7–8, 14–15, and 28, disease screening and treatment for any issues found, and a formal clearance assessment on day 30. Temperature should be maintained at 20–24°C throughout. The 30-day koi quarantine program in KoiQuanta automates all scheduling and logging for this protocol.

How do I set up a quarantine system from scratch?

You need: a tank of 200–500+ gallons (depending on fish size), established biological filtration (pre-cycled before fish arrive), aeration at minimum one air stone per 100 gallons, a reliable heater if water temperatures are variable, and a lid or cover. Set up and cycle the filter before you need it: run a sponge filter in your main pond and transfer it to the quarantine tank when fish are coming. This is faster than cycling from scratch and gives you immediately active biological filtration.

What should I test for during the 30-day quarantine?

Test ammonia and nitrite daily during the first two weeks, then every 2 days during weeks 3–4. Test pH and KH weekly. Log temperature with every test. Conduct physical examinations at days 7–8, 14–15, and 28, looking for external parasites, ulcers, fin damage, and abnormal behaviour. If you're a dealer with disease screening capability, a gill and skin scraping at day 7 adds meaningful confidence to your assessment. KoiQuanta's quarantine tracker logs all test results and schedules examination reminders automatically.

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Sources

Associated Koi Clubs of America (AKCA)
Koi Organisation International (KOI)
University of Florida IFAS Extension Aquaculture Program
Fish Vet Group
Water Quality Association

Execute Your Next Quarantine With KoiQuanta

The complete koi quarantine guide gives you the protocol. KoiQuanta gives you the tools to execute it correctly, log every step, and generate the records that prove it was done right.

Start your free KoiQuanta trial and set up your first quarantine protocol today.