How to Quarantine New Koi: A Step-by-Step Guide for Pond Keepers

Every koi keeper eventually faces the same moment: the box arrives, the fish inside is beautiful, and the pond is right there. It is so tempting to float the bag and let it swim. Don't.

Quarantining every new koi before it joins your main pond is the single most effective thing you can do to protect the fish you already own — and the one you just bought. We say this as people who sell koi for a living, and who quarantine every fish that comes off a plane from Japan for several weeks to a month or more before it goes anywhere near a customer.

Why we're this insistent

Even koi from excellent breeders can carry parasites or bacteria at levels their own immune system keeps in check. Shipping is stressful and stress suppresses immunity, so a fish that looked perfect at the farm can show flukes, an ulcer, or something worse three days after arrival.

If that happens in a quarantine tub, you treat one fish. If it happens in your pond, you may be treating twenty — and our team has been called out to clean up that version more times than anyone would like.

Quarantine is not an optional luxury for careful people. It does four jobs: it lets the fish adjust gradually to your water, it lets you inspect it closely, it gives it time to regain strength after shipment, and it protects everything already in your pond.

Setting up the tank

Nothing elaborate. A food-grade stock tank or a 100–300 gallon tub is plenty. What matters is the equipment:

• A cycled filter. Seed it with media from your main pond filter a few weeks ahead so ammonia and nitrite are at zero from day one. A biofilter needs five things at once — alkalinity, oxygen, an ammonia source, flow, and no sterilizing chemicals. If your media is still stark white after a few weeks instead of darkening to tan, the filter is not establishing and something on that list is missing. Aim for KH 100–150 ppm, pH steady between 7.5 and 8.3, and ammonia at or near zero.
• Strong aeration, running constantly. Stressed fish need more oxygen, not less. Every holding bowl in our shop has an aerator in it before a fish goes in.
• A secure cover. New koi jump, especially in the first 48 hours.
• Shade and quiet. A dark, calm corner lowers stress considerably.
• The right dechlorinator. More on this below — it matters more than people think.

Salt at 0.3% — and the number most people get wrong

We run quarantine at 0.3% salinity. The way we explain it: you're putting the fish in a hospital bed. Raising salinity reduces the osmotic gradient across gills and skin, so the fish spends less energy on water balance and more on recovering.

Here's the arithmetic, because a lot of published figures are wrong. 100 gallons of water weighs about 834 lb. 0.3% of that is 2.5 lb. So 2.5 lb of salt per 100 gallons — about 25 lb per 1,000 gallons. The commonly repeated "3 lb per 100 gallons" is closer to 0.36%, which is higher than you meant.

Handy sanity checks: 1 lb per 100 gallons is roughly 0.12%; 1 lb per 50 gallons is roughly 0.24%.

How to add it:

• Dissolve it in a bucket of tank water first. Never broadcast dry salt — undissolved crystals sit on the bottom and a fish resting on them takes a real burn.
• Add in two or three portions over 12–24 hours rather than all at once.
• Measure your actual water volume. Most salt dosing errors are volume errors — a "30 gallon" tub holds less than 30 gallons once the fish, filter and rocks displace water.
• Use pure salt only. Pond salt, aquarium salt, solar salt or additive-free softener salt are all fine. No iodized table salt, nothing with anti-caking agents or added minerals.
• Salt doesn't evaporate. When you change water, re-dose only the volume you replaced.

And keep it honest with yourself about what salt does. It reduces stress and supports recovery, and it helps against some external parasites. It does not cure bacterial infection and it is not a substitute for identifying what's actually wrong.

Watch the chloramine

This one bites specifically in quarantine, and it's worth its own paragraph. Sodium thiosulfate — the active ingredient in a lot of cheap dechlorinators — handles the chlorine half of chloramine and leaves the ammonia behind. On an established pond the biofilter absorbs it. On a brand-new quarantine tub with a filter that isn't fully cycled, that released ammonia has nowhere to go.

Use a product that binds ammonia as well: Seachem Prime or Safe, ChlorAm-X, Amquel. On a new tub it's the difference between a treated water change and an ammonia spike.

The first 48 hours

Float the sealed bag for 20 to 30 minutes to equalize temperature. Then open it and add a little tank water every 5 minutes for about 20 minutes. Move the fish across without the shipping water — never pour that into your system.

Then leave it alone. Lights off the first evening, no feeding for at least 24 hours. Most new arrivals sulk on the bottom for a day or two; that's normal after a flight. It also helps to know the fish arrived empty — we fast koi for a full seven days before shipping, so there's less waste in the bag and less ammonia in transit.

What we watch for

Clamped fins. Lethargy. Flashing or rubbing. Gasping. Redness or sores. Excess mucus. Abnormal swimming. A fish sitting alone, hiding, or not responding normally.

Two specific things to take seriously. An unusually thick slime coat is not a healthy fish — a normal slime coat is good, but a heavy one signals acute stress or a toxic exposure. And popeye with the mouth stuck open is an emergency. We have watched that sequence run its course in a day: bottom sitting and clamped fins, then bulging eyes and a mouth held fully open, then dead. That is acute systemic failure, not a mild parasite problem, and it needs the whole system evaluated immediately.

Brown gills are worth noting too. Koi gills are red. After death they can go white as blood leaves. Brown is unusual and tells you something.

Parasite treatment

Every koi we import is treated for parasites during quarantine. If you're treating your own new arrival, the important detail is that one dose is not a course.

Praziquantel doesn't burn parasites off — it interferes with their muscle and nerve function, paralyzes them and causes them to detach. Flukes start dislodging within 3 to 6 hours, most die within 24 to 48, and full effect takes 3 to 5 days.

But gill flukes lay eggs, and the eggs survive the treatment. New flukes hatch 4 to 7 days later, faster in warm water. That's why a second dose at 5 to 7 days is not optional — without it you've knocked down the adults and handed the next generation a clean tank. Skin flukes are live-bearing, with no eggs waiting, so a single treatment more often does the job.

If a treatment seems to fail, resistance is rarely the reason. Far more often it's egg hatch, mucus protecting the parasites, flukes tucked inside gill folds, or a repeat dose that never happened.

Two practical notes: clean water helps the medication work, so do a partial water change and clean the filter before treating. And turn off carbon filtration, UV and any protein skimmer during treatment — they'll strip the medication out.

Also know what praziquantel doesn't cover: anchor worm and other crustacean parasites, internal roundworms, bacterial disease, water quality problems, toxin exposure. If a single fish keeps declining while everything else is healthy and parasite treatment isn't helping, stop escalating parasite treatment and start looking at internal disease. Where it's available to you, a skin or gill scrape under a microscope beats guessing.

How long?

Thirty days minimum. Longer is better if you're adding to an established collection.

The clock restarts if you add another fish partway through, so batch your arrivals — if you're buying more than one from us, tell us and we'll ship them together for exactly this reason.

Test pH, ammonia and nitrite through the first week, and keep testing after that.

On water changes, one correction to the advice you'll read elsewhere: a water change is what you do when your filtration can't keep up, not a ritual on a calendar. If the quarantine filter is properly cycled and ammonia and nitrite are reading zero, you don't need to be swapping water for the sake of it. If they aren't at zero, change water until they are — and stop feeding while you're chasing it, because feeding is what's producing the ammonia.

What you must not do is stop testing because yesterday's numbers were fine. We have seen a holding tank where Thursday's readings looked stable, so Friday's water change got skipped. The fish were active at four that afternoon. They were all dead the next morning. Testing is what tells you which day is which.

Before the fish joins the pond

It should have been eating well for at least a week, show no marks, ulcers or missing scales, and have stable water behind it. Match the tub temperature to the pond within a couple of degrees, and move it in a bowl rather than a net to protect the slime coat.

Quarantine is unglamorous and it takes patience. It is also the difference between a collection that grows every year and one that starts over every time a box arrives.

Questions about a new arrival? Call the shop at (786) 304-2352 — we'd rather talk you through it than treat it later. Salt, dechlorinator, test kits and treatments are in our koi care collection.