Fish Quarantine Step-by-Step Guide

The most important things to have when it comes to fish quarantine, is having basic knowledge of the fish that you are quarantining. So many people skip that step, and they have fish that are either inappropriate for a reef, inappropriate size for the tank they’re getting put into, or are complete disease magnets and people are not prepared for that.

 Things to know prior to quarantining

What does your fish eat?

What would your fish normally eat in the wild and are you able to replicate that? Some fish like large angel fish for instance only eat sponge and that’s a really hard thing to provide in a tank environment.

Is it desease prone?

If your fish is disease prone, which diseases and/or parasites is it prone to? Powder tangs, for instance, because of their thinner scales, are really prone to ich.

If you know these things going in, it'll be easier for you now that you have this knowledge in your arsenal.

 Step 1: Choose Healthy Fish

These are some things to look for when you're trying to find a healthy fish

1. Is it eating?

I know that’s a very simple question, but sometimes fish are very stressed out and they are not eating right away when they first come in. If they are when you see them eating at an LFS it’s a fantastic sign.

2. How is it swimming?

Are they pacing the tank really quickly? Are they hiding in a corner? Are they being bullied? These are some things to watch out for as well. Even bullying in fish can be a sign of an unhealthy fish.

3. Pinched belly

If you see a fish at an LFS that is really thin and has a pinched belly, there’s a good chance that there could be internal parasites. If it ends up not eating in quarantine due to stress, it’s going to have a hard time recovering. This holds especially true for mandarins. If you buy a skinny mandarin it’s probably not going to end well.

4. How is it breathing?

Breathing is a huge sign for a lot of illnesses. If a fish is breathing heavily then that could be one of the first indicators for something bad.

5. What do their eyes look like?

If the fish has clear eyes that’s a great sign. If there’s even a little bit of cloudiness in the eyes, that combined with the heavy breathing, are symptoms of incredibly fatal diseases.

 Step 2a: Equipment Shopping List

A good thing to do before you get your fish is to buy your medication and equipment ahead of time. It’s not fun to wait on a delivery truck for your supplies and just have your fish sit in the tank for two days. It’s bad timing and not good practice.

This shopping list is pretty easy to adhere to. This will be all the basic stuff you'll need.

1. Seeded Biological Filtration

The first thing on the list is a seeded bio sphere, or just a sponge that you have soaking in your sump for a month or so. Something that will give you a little more stability once you set the tank up. It’ll help so that you don’t have to do water changes quite as often. Hopefully you’ll only have to do water changes weekly instead of every 2 days.

2. Live Bacteria

Live bacteria is also something that helps keep the tank stable along with the bio filter

3. Tank and Lid

This may seem obvious, in order to house fish you need to have a tank. Make sure when you buy your tank that it will be the proper size for the fish that you are getting, the space you will be putting it in, and the amount of maintenance that you are willing to put into it.

I like to do anything from a 10-50 gallon tank for quarantining, just because it will make water changes easier. You’re only going to be doing a small handful of fish at a time so you don’t want to crowd a tank. Ideally you just have one fish in one tank that you can keep an eye on.

4. Hang-on-back Power Filter

You’ll need one hanging power filter, 2 if your tank is on the longer side. This just helps with water flow and the flow of oxygen.

5. Small Power Heads

These are mainly for larger tanks, or if you’re acclimating a fish like an Achilles tang that actually enjoys a lot of flow.

6. PVC hiding spots

You’re going to need a lot of PVC for them to hide in. Nothing too expensive, just whatever is on sale at your local hardware store. 2-3 inch tubes tend to be the best because fish like to hide and squeeze into little spaces.

7. Ammonia Alert Badge

An ammonia alert badge is a simple little thing, but it’s a great visual aid. It’ll tell you if you even have small traces of ammonia in your tank. These normally will last you around a year or so before needing to be replaced.

8. Heater

This heater does not need to be anything fancy. Just make sure the heater is appropriate for the tank size.

9. Grounding Probe

Due to some of this equipment being cheaper than what you may be used to dealing with, you might want to consider getting a grounding probe. It’s an easy piece of equipment that makes sure your fish won’t get electrocuted if something goes wonky with any of the electrical components.

10. Lighting (optional)

We have been using additional light sources for our tanks, but it’s not completely necessary. Ambient room lighting is usually more than enough. In my old apartment, I acclimated fish in the space on top of my dresser because that was the most convenient place for the tank, and we did it without additional lighting and everything was fine.

11. Fresh Saltwater

You’re going to need lots of this, and have it on hand before your fish arrive and also for emergency water changes if needed. If a fish is breathing really heavy, you shouldn’t have to make them wait 45 minutes while you make more salt water.

12. Poly Pads

I like to use poly pads to act basically like a filter sock and then hang on the back filter.

13. Quarantine-only Hose and Nets

You’re going to want to have separate hoses and nets for your quarantine, mainly because you don’t want to risk contaminating the stuff you use in your display or vice versa if one of your fish does have a disease.

14. Activated Carbon and Filter Bag

After you run medication you will be using carbon for a week or so to suck out that excess medication before switching to any new medications.

15. Thermometer

Just another visual aid so you can see if everything is running smoothly. However, you might want to have multiple tools for temperature measurement, only because there can be inconsistencies. I like having a thermometer and a temp gun just so I can check them against each other

 Step 2b: Medications Shopping List

1. Prime/Amquel Water Conditioner

This will help detoxify the ammonia, nitrites, or nitrates if you need to. It’s a great "water bandaid" to have on hand

2. Prazipro

This medication treats a lot of internal parasites, as well as, worms and flukes.

3. Formalin

This will take care of most external parasites. If bought on amazon, the bottle will say Formaldehyde but will have Formalin in parentheses on the bottle. It’s a great product to have and is very gentle. Make sure to hide it and store it very well because it is toxic.

4. Copper

There are a couple different kinds of copper to choose from. This is normally used to treat ich and velvet.

5. Furan-2

This medication is good to use for any bacterial issues

 Step 3: Setting up

This will end up being one of the easiest saltwater tanks you will ever set up. When it comes to placement of your tank make sure to set up in a quiet area if you can, somewhere that’s not super bright and doesn’t get a lot of traffic. A bedroom is always a good option, a dining room that no one really goes in, that sort of place.

Remove the carbon from the power filters, you’re not going to want that right away because you will be adding medication. The only thing I put in the power filters are the sponge or bio filter mentioned previously, and a poly pad to act like a filter sock to catch any big debris. Basically everything that the filter comes with, set aside for now.

Next install your filter, heater, and power heads if you’re using them, along with the ammonia alert badge, thermometer, and grounding probe if you’re also using that. Then add in all your little PVC hiding spaces, make sure to add enough of them into the tank for them to have multiple hiding spots. Finally, go ahead and add in your saltwater and bacteria and bring your tank up to temp.

After all of that you are ready to add in your fish, cover the tank, and start treatment

 Step 4: Treatment

So now we are going to get into actually treating your fish. I’m going to give you the steps that I like to follow, along with some additional steps as well.

Step 1: Prazipro

I usually do Prazipro first to get rid of any internal parasites or worms. This treatment is really gentle. Most fish that come in, if they have something, will ususally be treated by the Prazipro alone.

Treatment includes:

- 1 teaspoon of Prazipro per 20 gallons for 1 week

- If you do a water change during that time make sure to replenish the amount that you took out. So, for example, if you did a half water change on a 20 gallon tank, you would add another half teaspoon of Prazipro afterwards.

After I’m done running prazipro I run carbon in the power filter for about a week just to pull out any leftover medication, and if you have a UV filter in your tank this is where you can turn that on as well

Step 2: Formalin

After running carbon for a week and doing a water change I like to take the carbon out and run Formalin. With Formalin I feel like I have all of my bases covered because it covers pretty much all of your external parasites. Anything from ich to velvet, brook, and uronema. If you’re using copper, that really only treats ich and velvet.

Treatment includes:

- 5 seperate treatments over the course of 10 days, accompanied by 50% water changes

- Every other day, do the water change, then add 1mL of Formalin for every 10 gallons of water

- Make sure to wear gloves when handling this chemical, due to the toxicity

This treatment works great, and is a great blanket treatment for all of my fish. You can use copper instead for ich and velvet if you want to. Depending on the brand you are using, that will be a 2-4 week bath. You can find copper at pretty much any LFS. It’s pretty easy to come by if you’re uncomfortable purchasing Formaldehyde for any reason.

 Step 5: Observation

Now that we have covered the treatment schedule, let’s talk about what we are going to be the whole entire time, and that is observing your fish.

A lot of the things you are looking for are similar to what you would look for in a healthy fish first starting out. You’ll want to see if their eyes are clear, if they’re breathing normally, if they’re swimming normally. You mainly want to watch and make sure they aren’t hiding or scratching, and you’ll also want to see if they are eating well and are having healthy bowel movements. Healthy bowel movements is a great indicator as to whether or not your fish have something weird going on.

A couple of things that are normal that may seem odd are: hiding, fish will usually like to hide even if it means curving along the walls of the PVC. This is a very unnatural environment for them, don’t let it worry you too much as long as your fish is eating. However, sometimes they won’t even let you see them eat so stand back a few feet and watch from a distance. If you hide slightly out of view, it will usually make them more comfortable and they’ll come out. If you continuously inch closer each time you feed them, they’ll eventually realize that you mean food and they’ll come around to being comfortable around you.

 Step 6: Food and Feeding

Speaking of food, we use a variety of foods during quarantine so you can see exactly what your fish like to eat and don’t like to eat. This helps to ensure that you aren’t polluting your tank. We feed, primarily, Sustainable Aquatics: Hatchery Diet pellets. These are fantastic. Most fish take to these before they will take to most other kinds of foods.

I like to give a variety of frozen foods during quarantine as well. Mysis shrimp is great due to the high protein levels. You can do some food preparations with sponge if you are trying to quarantine angel fish. Spirulina brine is another good one for the finicky eaters for some reason, also blood worms interestingly enough, I’ve had really good luck with getting butterfly copper bands to eat blood worms.

If you are acclimating Tangs, or herbivores of any variety, I recommend using an algae clip and providing a few different kinds of seaweed if you can.

When it comes to medicated foods, should you need them, I like to use Dr. G’s frozen foods. They have an antibacterial and an anti parasitic that most fish tend to go after pretty readily. I’ve had pretty bad luck with medicated pellets. Most fish I’ve found don’t care for them, I don’t know why exactly.

 Step 7: Acclimating into your display

Once you are confident that your fish are healthy, it’s time to acclimate your fish into your display tank.

If it’s your first fish, that’s not a problem, you can just acclimate them and add them right in. If you already have fish and are concerned with aggression, you can keep lights out for a couple of days if you need to. Sometimes rearranging rocks can help because it messes up territory lines and acts as a reset button in that regard.


That pretty much does it for a step-by-step quarantine procedure, hopefully that gives you a little more confidence. Good luck and Happy Reefing!

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