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.

Refugium 1

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.

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.

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.

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

Empty center chamber with rubble rock

Chaetomorpha (aka Spaghetti Algae or "Chaeto") w/ Nano-Glo attached

Chaetomorpha (aka Spaghetti Algae or "Chaeto") w/ Nano-Glo attached

DT's Live Marine Copepods

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

Hang-on refugium with sand and live rock

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

Side sketch of what the fuge will look like

Top-down view of how we will integrate the new refugium into the aquarium system

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


  • Standard 10-gallon glass aquarium (20" x 10" x 12")
  • 2 pieces of glass: 1 x 9.75" x 8", 1 x 9.75" x 7"
  • Tunze Silicone Sealant
  • Sand
  • JBJ Macro-Glo Refugium Light

Plumbing parts

  • 3' of 1" PVC or Flexible PVC
  • 2 x 1" Slip elbow
  • 1" Double slip bulkhead
  • 3 x 1" Slip tee
  • 2 x 1" Slip union
  • 1" Slip cap
  • 1" Slip strainer


  • 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.

refugium 5

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

Diamond hole saw attached to the drill

Shot of the freshly cut tank

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

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

Tank with tape markers for the baffles

Baffle taped and sealed with silicone

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

Water testing the refugium

Converted refugium—Mr. Aqua aquarium

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.

Small "durso" pipe for the water leaving the refugium

Small "durso" pipe for the water leaving the refugium

Plumbing fitted for testing

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!

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

Refugium fitted with the JBJ Macro-Glo fixture

Up and running refugium

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.