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Q11089 - HOWTO: How to Setup a Refugium by Daniel S., Reef Squad
For a few years now, refugiums have been all the rage in marine aquariums, and with good reason. Refugia are excellent natural filters with a lot of benefits.

So, what exactly is a refugium, how does it work and how can one be installed on your system? Read on and we'll show you how simple it can be. This article will provide some good information for beginning as well as more advanced hobbyists.

Simply put, a refugium is an area in an aquarium system where microorganisms can live and breed without predators. Copepods, baby brittle stars and the like are able to "take refuge" in this area, reproducing safely. Live rock rubble and/or deep sand beds are often used to create a safe habitat for these animals. Some hobbyists like to use mud in their refugium. My personal preference is fine sand.

Aquarium Refugium
Refugiums are also commonly used as a place to grow certain species of macroalgae. Nuisance algae are a common issue for aquarists. Designating a place for algae to grow where it can be managed prevents algae from taking over the main tank. Algae in the refugium absorb nutrients like nitrates and phosphates from the water, "banking" them inside themselves. The aquarist then prunes the algae, removing the banked nitrates and phosphates from the system. In this way, phosphates and nitrates are kept low naturally, without chemicals or purchased media. In addition, the macroalgae serves as a great hiding spot for microorganisms.

Refugiums are a great place for a deep sand bed, which can help lower nitrates. A deep sand bed creates a hypoxic area (low in oxygen) where nitrate-eating bacteria thrive. These bacteria convert the nitrate into nitrogen, which then leaves the system as a gas. For more information on deep sand beds, click here.

Cryptic zones, or dark refugiums, have also started to grow in popularity. The basic idea is to create an area for filtration that receives little to no light. Live rock is piled up, creating a place for sponges and other non photosynthetic filter feeders to grow. This type of filter gets better with age, taking a significant amount of time to mature. Hobbyists are starting to experiment more and more with ways to incorporate cryptic zones into their system, often partitioning off areas of a sump or refugium and protecting it from any significant light source. We're not covering cryptic zones today, but it is still good food for thought when considering a refugium.

Now that you know what a refugium is, I hope you can also see the many good reasons for having one. Many fish, like mandarin gobies, feed naturally on microorganisms that are difficult to keep in supply without a refugium. Corals benefit from the consistent food source. Algae are given a safe, out-of-sight place to grow, which helps reduce nutrients. Refugiums are also commonly run with the lights on opposite of the display. As photosynthesis occurs, carbon dioxide is used up and oxygen is produced, which raises pH. So, keeping a refugium on a reverse daylight period helps stabilize pH.

If you have a nano or mid-size all-in-one aquarium, setting up a refugium is simple. For the Solana tank we're setting up here, all we need is some live rock rubble and JBJ's Nano-Glo Refugium Light. This setup also works for most JBJ Nano Cubes and Oceanic BioCubes.

First, empty out the center chamber and place some rubble rock on the bottom.

Next, place a small ball of chaetomorpha (aka Spaghetti Algae or "Chaeto") algae inside the chamber.

JBJ Nano-Glo Refugium Light
JBJ Nano-Glo Refugium Light
Then attach the Nano-Glo to the clear back chamber with the magnet on the inside. I plugged the Nano-Glo into the moonlight socket on a Zilla Power Center to run opposite of the daylights.

That completes the setup, although I did add a jar of DT's copepods to seed the fuge with critters. I also put a filter pad over the refugium to prevent light from spilling into my bedroom.

Empty center chamber with rubble rock Chaetomorpha (aka Spaghetti Algae or "Chaeto") w/ Nano-Glo attached DT's Live Marine Copepods
Empty center chamber with rubble rock Chaetomorpha (aka Spaghetti Algae or "Chaeto")
w/ Nano-Glo attached
DT's Live Marine Copepods

Next, let's look at using a hang on refugium.

Hang on refugiums are a good choice for systems that do not have a sump. I prefer the hang on method versus an in-tank refugium because a hang on will not take away from the beauty of the display. Setting up a hang on refugium is simple.

First, fill the refugium with freshwater to test for leaks. It's better to discover a leak before you've got the thing hanging over your carpet. Once you're sure it can hold water, dump the freshwater out.

Next, add sand and live rock rubble to the empty refugium. I've used a deep sand bed here but anything around 3" deep will work. Adding sand before water prevents the tank from turning cloudy.

Mount the refugium onto your aquarium. A small pump will sit inside your tank to feed water into the refugium. Water will then drain by gravity back into your tank. This helps keep the small copepods from getting chopped up on the way back in. The last piece of equipment to add is a light. For our demonstration, we are using JBJ's popular Macro-Gro Adjustable Refugium Light.

Finally, fill the refugium with saltwater and Chaetomorpha and turn on the pump. Your hang on refugium is up and running in less than 15 minutes!

Hang-on refugium Hang-on refugium with sand and live rock JBJ Macro-Gro Adjustable Refugium Light
Hang-on refugium Hang-on refugium with sand and live rock JBJ Macro-Gro Adjustable Refugium Light

If you have the space, the best way to run a refugium is in a dedicated tank attached to your aquarium. Some hobbyists prefer placing the refugium above their display tank so gravity will naturally return the water back into their aquarium. This avoids the copepod blender problem mentioned earlier. It's a nice gesture, to be sure, but not necessary. Microorganisms will make it safely into your aquarium, even through a return pump. Those that do not become food.

A refugium can be a designated area in an existing sump or setup in a separate tank attached to the system. For this demonstration, we'll do the latter; practically building a fuge from scratch to attach to an existing system.

Not everyone has the time or inclination to build a custom refugium. If this sounds like you, not to worry: there are some great prefab choices to consider. The Berlin sump can serve as a refugium on a larger tank. Alternatively, Precision Marine makes some very clean sumps that have refugium chambers. Of course, if you like to tinker with your tank, like I do—or are interested in learning more—read on.

Setting up this fuge requires you to know some basics about setting up and plumbing a sump system. If you're not yet familiar with sump or wet/dry filter plumbing, you're in luck: we've got a nice article here for you to reference.

I like to start with a few sketches of the build, brainstorming as I go to think of (and resolve) potential problems. These sketches give me something to reference during the build to avoid potential mishaps.

Side sketch of what the fuge will look like Top-down view of how we will integrate the new refugium into the aquarium system
Side sketch of what the fuge will look like Top-down view of how we will integrate the new refugium into the aquarium system

It's time to get started. For the refugium and stand, we will need the following parts:

  • 2" x 4" (approximately 6' worth)
  • Wood screws
Refugium Plumbing parts Tools
  • Cordless drill
  • 1 x 1 3/4" Diamond hole saw
  • Electrical tape
  • Safety glasses
  • Gloves
  • Measuring tape
  • Masking tape
  • Sharpie
  • Rubbing alcohol
  • Level square
  • Razor blade
  • Pipe cutters
  • PVC glue
The first thing we are going to do is drill the glass aquarium.

It is extremely important that you understand this procedure can result in a broken tank. To that end, we make the following disclaimer: this how-to is for educational purposes only. We are not liable or in any way responsible for anything you do with the information contained herein. If you do not want to risk cracking your would-be refugium, you may want to contact a professional to drill the tank for you. Many glass shops and aquarium stores will provide this service for a small fee.

I've personally drilled many pieces of glass and only once had the glass actually break. Thankfully, a 10-gallon aquarium only costs about $10, so this is a great project to learn the ropes of drilling glass.

Take the Sharpie pen and mark the area you want to drill. In the photograph below, you'll notice the drill marks (the "X") are not too close to the edge. The closer you get to the edge, the more likely you are to crack the tank. A good rule of thumb is to drill at least as far away from the edge as the diameter of the hole.

Next, cover the inside of the tank around the hole you've sketched with electrical tape. This helps prevent the glass from chipping. You probably also noticed the horizontal tape in the photograph. It marks the minimum height the hole has to be so the bulkhead is above the sump wall.

Place the aquarium on its side and place a towel inside of it. Make sure your drill is charged and have a garden hose ready.

Electrical tape covering the inner side of the tank Aquarium on its side with a towel inside
Electrical tape covering the inner side of the tank Aquarium on its side with a towel inside

It's time to drill… but first, a word of thanks to all the spouses and significant others who have been suckered into helping hold garden hoses, taking down canopies, dealing with water on the floor, and so on. We appreciate the sacrifices you make for our hobby!

Turn the drill on and move it toward the tank wall as straight/vertical as possible. When the drill makes contact with the glass, start wetting the area with the hose. DO NOT PUSH the drill through the glass. Instead, hold the drill in place and slowly grind the glass out. If you push down with anything but the slightest force, the tank will crack. Keep the hose water flowing over the surface of the glass to keep it cool as you drill. In a few minutes you will break through to the other side and be ready to go.

Diamond hole saw attached to the drill Shot of the freshly cut tank
Diamond hole saw attached to the drill Shot of the freshly cut tank

Next, we're going to install the baffles. Baffles are walls inside the sump that slow down the water and force bubbles to rise, detritus to fall and allow water to pass through.

Measure your refugium-in-progress to determine where you'll place the baffles. For this demonstration, we will place baffles about 4" from the end. Be sure to leave enough room to fit a bulkhead. Draw lines on the outer bottom and sides of the tank with a Sharpie to mark where the baffles will go. Clean the area where the baffles will go with rubbing alcohol.

Cover the tank about ¼" from where the baffles will be using masking tape. This will make a sloppy silicone job look much cleaner.

We are ready to install the baffles. The smaller baffle will be placed next to the hole in the tank; the larger one will be positioned on the opposite side.

A quick note about silicone: not all silicone is created equal.

Don't just stroll into your local hardware store and grab the first silicone you see. Just because it says "100% silicone" on the package does not mean it's aquarium-safe. Commercial silicones often include mildewcides that can harm the animals in an aquarium. Look for silicones that state they are "aquarium safe," "food grade," or "FDA approved" on the label.

Tunze Silicon Glue
Tunze Silicon Glue
Since I do not want to take chances with the animals in my care, I've opted for Tunze brand sealant.

Put a small bead of silicone on the bottom of the baffle and push it gently into place on the line you've drawn. Make sure the baffle is perfectly in line with the marker lines.

Next, tape the top of the baffle to the tank to hold it in place (see photograph). Then, put a nice bead of silicone across the sides and bottom of the baffle. Double-check to make sure your lines are straight with the square.

Lightly moisten your finger with water and run it along the bead of silicone. Make sure the silicone gets into the seams and that you clean up any excess. Wait 60 minutes. Then, run a razor blade along the line between the tape and silicone. Remove the tape.

Repeat this process for the smaller baffle.

Tank with tape markers for the baffles Baffle taped and sealed with silicone
Tank with tape markers for the baffles Baffle taped and sealed with silicone

With both baffles in place, it's time to allow the silicone to cure. Although it may be ready in as little as 24 hours, I recommend waiting a whole week, if possible. Silicone can release harmful substances, like ammonia, into water. The likelihood this will happen will dissipate the longer you allow it to cure. Generally speaking, the less it smells, the better.

After giving the silicone plenty of time to cure, it's time to perform a water test.

Take the refugium outside and begin filling the first compartment with water. If a tiny amount of water seeps through the seams, it's not a deal breaker.

We are primarily looking to make sure the baffles are securely held in place. Once you are sure the first baffle is secure, continue filling the aquarium until the second chamber is full. Let the tank sit for awhile before emptying.

For the stand, build a simple frame with legs. Double-check to be sure the refugium's outlet (with the stand) is tall enough. Our refugium is going to gravity drain into a sump, so it needs to be taller than the side wall of the sump. The sump we're using for this demonstration is a Mr. Aqua Aquarium that we converted into a sump using the same methods as our refugium build.

Water testing the refugium Converted refugium—Mr. Aqua aquarium
Water testing the refugium Converted refugium—Mr. Aqua aquarium

The next step is to get the refugium mounted in the sump.

Place the stand inside the sump and then set the refugium on top of it. Place the sand bed inside the center chamber along with any live rock rubble. I prefer to place the live rock right after the first baffle so that the sand bed does not get disturbed by the cascading water.

Now we need to plumb the refugium.

Thankfully, this system already has two drains coming from the main tank so the refugium is easily fed. On the inlet to the refugium (the drain coming from the aquarium), I have placed a slip elbow, a 1" union and a short run of PVC pipe that I cut to size with a pipe cutter. Unions are important so we can disconnect the pipes if we ever need to remove the refugium from the stand.

I have created a small "durso" pipe for the water leaving the refugium. This allows air to escape and helps make the refugium quieter. A short length of PVC is cut to attach the slip tee to the inside of the bulkhead. Then another short piece of PVC is used to attach the cap (with holes drilled in it) to the top of the tee. A strainer is attached to the bottom of the tee to prevent macroalgae from entering the sump. I just slip fit this together without gluing since it doesn't really matter if it leaks.

Now we need to get the water from the refugium into the sump.

Another union is placed right after the bulkhead so the plumbing can be removed, if needed. A 45-degree angle pipe is used to move water down into the sump. Depending on your application, an elbow will work just as well. I initially wanted to mount the refugium sideways in the rear of the stand, but it was about ½" too long. While this plumbing arrangement isn't ideal, it still has space in the center for reactors and supplemental storage.

Slip elbow, a 1" union and a short run of PVC pipe Plumbing fitted for testing
Small "durso" pipe for the water leaving the refugium Plumbing fitted for testing

We are finally ready to test the new system.

I like to fit all the plumbing together without gluing to make sure everything works as planned. There might be a drip here or there, but it gives me a good idea of how everything will work. After the test run I'll stop the flow and glue all the parts in place. There is nothing more frustrating than getting this far along only to realize you've made a miscalculation somewhere in your design.

Now that everything is up and running smoothly, you can go ahead and put your refugium light in place. We're actually using the same Macro-Glo fixture that we used for the hang on demonstration. You can see in the photograph how easily it clips on the side of the tank

I'm going to use some of Brightwell's Microbacter7 and copepods to kick start the refugium, but you can let it turn biological naturally over time. A common trick is to get a cupful of sand from another reefer's aquarium to help seed the new filter.

I am going to mount my temperature and pH probe in the refugium using this cool little magnetic probe holder from Eshopps. The probes will go in the first chamber before the actual refugium.

And there you have it!

Eshopps Magnetic Probe Holder
Eshopps Magnetic Probe Holder
The brand-new refugium is online, soaking up nutrients and breeding microorganisms for my fish to eat. I've already seen a few baby brittle stars cruising around eating up waste. I haven't tested the phosphate since putting the filter online, as mine was already low, but I expect from past experience to be purchasing less phosphate media from now on.

Refugium fitted with the JBJ Macro-Glo fixture Up and running refugium
Refugium fitted with the JBJ Macro-Glo fixture Up and running refugium

I hope this article was informative and fun. I had a great time with the project. As always, if you have any questions, feel free to call or email the Reef Squad. We're here to help you succeed.
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Approved Comments...
Great article!!! Very detailed and informative!!! Approved: 9/30/2014
Very detailed and informative ! Approved: 12/15/2013
Very informative. Gave an explanation of many types of refugium and h ow to implement Approved: 4/28/2013
I was glad to see it from beginning to end with pics thanks! Approved: 2/20/2013
I thoroughly enjoyed reading this article! I am in the process of building a refugium as well. I found the description of securing the baffles and drilling a hole to enable gravity to bring the biologically filtered water into the main system was very informative and helpful. I certainly will take into strong consideration the topics discussed for my own 40 gallon refugium. Thanks! Approved: 1/22/2013
easy to understand Approved: 1/22/2013
Very informative. Approved: 12/26/2012
Great guide. I search this online then i became a member. Could you tell me which pump is good for it? Approved: 10/29/2012
Great step by step guide. Approved: 4/29/2012
I would like to know how many times the tank should empty per hour. (Optimal Flow) per hour Approved: 4/4/2012
GREAT, well explained topic, definitely helped me out and gave me plenty of ideas for my upcoming set up Approved: 4/1/2012
Great and easy to take in but I am confused about flooding Approved: 11/14/2011
It is written with the beginner in mind. While I have read and asked many sources, I still need the step by step explanations with pictures. These articles are making Marine Depot my main source for product purchases. Approved: 11/12/2011
Now I know what a refugium is! Approved: 9/5/2011
as a seasoned fresh keeper i am looking for ideas on going reef on a budget! this is great! you guys are the best! Approved: 4/25/2011
I like the idea of keeping my tank as natural and chemical free as possible. Approved: 1/21/2011
The article was great! I just have a question. How big should your refugium be to get the benefits of bio-filter (phosphate removal)? I have a 40gal breeder and a 2gal refugium with a flow rate of only about 150gph. I dont think this is enough. I have bunches of lil critters in my refugium and my Chaetomorpha is growing well, I just dont think I am getting much bio-filter out of such a small refugium compared to my tank size. I am going to make a bigger one but How Big should it be? (Editors note: Hard to answer a question here, please send your question to for assistance). Approved: 11/9/2010
Great Article. Would like to know your thoughts on the amount of flow going through the refugium. We hear plenty on 10-30 times for circulation in the display tank, but what about the fuge? How much is too much to blow away all the copepods? Im at the Sump/Refugium stage in my build and am interested in this sites thoughts. Thanks Kev Approved: 10/18/2010
It seems to be well thought of. but my question is what type of seeweed can i put in refugium, i also will be using FIJI Mud and some rock. I have a Marineland R24B refugium which has a sump a refugium section and a return section to aquarium. Approved: 10/18/2010
great article. Unless I missed it there was no discussion of how to actually adjust water levels to prevent floods. But then that is more a sump thing anyway. Also (even though the first refugium was close), no real discussion of an in tank refugium. Perhaps that is because it is too simple. I see some comments here do mention cyano. With an external lit refugium running when you eventually get the dreaded red slime, you just kill the display lights for a few days untill the slime dies off. then adjust display lighting to where display stuff thrives but display cyano does not come back. my .02 Approved: 10/18/2010
I believe that all tha basis were covered and the DIY instructions were an unexpected and big plus. Approved: 10/18/2010
Great article that covers most of the essentials. Many thanks! Approved: 10/17/2010
Excellent article with good detail on the primary components of building a fuge. I do believe the latest research has demonstrated the amount of copepods negatively affected by return pumps is less than originally thought. I have used a few gravity-fed fuges, but the cyano issue is a problem. My latest project will combine a cryptic zone for sponges, an algae scrubber zone, a dsb/lr zone all fed from a drain zone with strong skimming. Some have had great success w/out skimming using the algae scrubbing, but I still prefer both skimming and vodka dosing. Im also using uv lighting and plan to experiment with ozone fed skimming. Approved: 10/17/2010
I thought the article was informative, but I was hoping it would discuss ways of dealing with some Refugium problems such as Cyanobacteria Approved: 10/16/2010
All of your articles are very well written and accurate. Im an intermediate aquariest and look forward to all your reef articles, there all very useful. Please keep them coming! Can you guys do something from setting up a large reef tank with refuge. How much live rock what size refugem how much sand, how much mud or sand in the refuge.what different medias to use and what reactors work best.And do you need a U.V. steralizer or Skimmer if you have a large enough refuge Approved: 10/16/2010
Very informative! Easy to follow. I have a refugium set up, but Im a little confused about how much light and how long to keep the light on. Ive read serveral articles about leaving the light on 24-7. To prevent the plants going asexual. Thanks for the great article. Steve Approved: 10/16/2010
Very good article on DIY refugium. Very well thought out and composed for a beginner. Approved: 10/16/2010
this is an excellent article,anybody wanting to build a refugium should be able to follow these instruction and have a nice refugium,its very well written and with the photos makes it even easier to follow....nice work Daniel S. the only thing I can add is that chaeto seems to grow better for me with a strong flow of water,most refugiums have a slow flow rate,so to keep my chaeto spinning,I added a powerhead in a separate refugium without sand,just for the chaeto Approved: 10/16/2010
Very informative and liked the pics to give you a visual example of set-up..... Approved: 10/16/2010
I like all of the parts being listed that you need, but I wish there were more picture of how the plumbing was done. When he talks about the "Durso" pipe, a picture would help me understand what he is talking about. Approved: 10/15/2010
I have been trying to start a Refugium and this was just the tips I needed. Thanks... Approved: 10/15/2010
Just make sure the 10 gallon you buy isnt made from tempered glass. That will crack when drilled. Approved: 10/15/2010
This is the best refugium article Ive ever read. Very thorough and easy to understand. Approved: 10/15/2010
Article Details
Created on 10/14/2010.
Last Modified on 10/15/2010.
Last Modified by Dot Yuson.
Article has been viewed 117359 times.
Rated 8 out of 10 based on 210 votes.
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