A Beginner’s Guide to Setting up a Refugium

There are many benefits to building or creating a refugium in your saltwater aquarium. It allows for additional surface area for beneficial bacteria to grow, which filters out nitrates and nutrients in an efficient and natural way. They also provide a habitat for small beneficial organisms so they can reproduce without getting eaten. Algae is also commonly grown in a refugium as an additional form of nutrient export. The algae uses the nitrates and phosphates, which come from food and fish waste, to grow. Then, the algae is harvested and the nutrients are successfully taken out. Having a refugium increases the overall biodiversity of your tank, which improves the wellbeing of the aquarium.

Pre-Planning Topics

  • Where:
    The location of where your refugium is going to be is very important and the first thing you need to decide. The best place for it is in a sump. Having a refugium in a sump is the cheapest and most beginner friendly option. If you do not have a sump there are other methods, but ultimately having a sump will be best. In your sump, you will most likely have two or three sections. The first section is where your intake is and where the protein skimmer is. The second section is where your refugium will be. And the third section is where the return pump that pumps the water back into your tank is located. You may have other kinds of filtration and equipment such as carbon, GFO, reactors, and dosers, but essentially the best place for your refugium is the last section of filtration. This ensure that any copepods or other organisms will not be filtered out before they get put into the tank and it allows your protein skimmer and other filtration to work more efficiently. There are certainly reasons to put the refugium in a different section, but putting it as the last stage is the most methodical place.
  • Budget:
    You must decide what your budget is for your refugium will be. How much are you willing to spend? It is possible to build a refugium with under $100, but there are benefits to spending more. With this in mind, consider what kind of media or substrate you want and also what kind of light you will use. Along with any crustaceans or organisms.
  • What:
    What will you put in the refugium? You can use plain sand which you can buy new or use left over sand. Another option is refugium mud, which is said to be better than regular sand. You could leave it at that or go further and buy rock or use left over rock. MarinePure blocks are perfect media for a refugium. They have a surprising amount of surface area for there size, which makes them a better option then rock. I do not recommend using live rock, as live rock will most likely have harmful pests and is much more expensive.  When it comes to algae, I recommend Chaeto or Chaetomorpha. This is the standard algae for refugiums, which is for a reason; it is easy to care for, grows fast, and is very effective. You can choose a different kind, but for a beginner, Chaeto is the way to go. This algae is not like the algae that you are scrubbing off your rocks or scraping off your glass. It is beneficial and not harmful or annoying. It is called macroalgae, while the pest algae is called microalgae. You will also need some kind of small crustaceans, such as copepods or amphipods. Along with phytoplankton to feed those organisms. AlgaeBarn sells their Ultimate Refugium Starter Pack that has everything you need to start your refugium that was just listed as well as beneficial bacteria for cycling a tank. It is great for beginner refugiums or for anyone starting a new refugium and is cost efficient as well.  Last, you will need a light. There are many options for refugium lights and depending on your standards and budget, it should not be too difficult to find the one for you.


After considering and planning the previous topics, you will be ready to set up your new refugium.

  • Step 1: Turn off your return pump and prepare the section where you will have your refugium.
  • Step 2:  Add your substrate and media. If you have chosen to use sand or refugium mud, put that in first and fill to about one to two inches of depth. Then add your rocks, MarinePure blocks, or other media you chose. You may want to rinse out your media before using it if it is new or has been sitting out for a long period of time.
  • Step 3: Put in macroalgae. You can wedge it under a rock or use string or a rubber band to keep it down. This way the algae does not have the possibility of being sucked into your return pump, causing a mess in your tank and a pump that needs to be cleaned out.
  • Step 4: Add copepods or amphipods. Pour them directly into the refugium section. You can even use a baster to spray them on to the substrate and rocks.
  • Step 5: The copepods will need food, which is what the phytoplankton is for. There is no trick to putting it in. Just pour it all into the refugium. If you bought the Ultimate Refugium Starter Pack, you can also add the bacteria, even if it’s not a new tank.
  • Step 6: Let the refugium settle. It is important that you wait a while before you turn your return pump back on. This allows all the crustaceans, phytoplankton, and possibly bacteria to get into the deep pores and crevices of your refugium media and not get sucked out by your return pump.
  • Step 7: Add light and set a timer. Mount your light so that it lights your refugium in a efficient way for optimal growth. Set the timer so that the light comes on when your main display light turns off.


Maintenance on your refugium is simple. Harvest the macroalgae every two to four weeks depending on how fast it grows. That’s about it. Simple, easy, and very effective.

Congratulations! If you followed these instruction and tips you will now have had successfully set up your refugium. You will soon see your algae grow and the positive effect of having a refugium for your saltwater aquarium.

84 thoughts on “A Beginner’s Guide to Setting up a Refugium”

    1. Rudy Brambier

      I found with proper lighting you don’t need and even get better growth on a reverse daylight schedule. That way you balance your Ph at night. A good grow light does not need to be on all the time.

    1. A quality light for a few hours a night, good flow, give it a shake once in a while to get the gunk off, and the chaeto will grow. If your fuge is under your tank in a regular stand, be sure you enough height between high output lights like the Kessil H360 and the water surface. That is my set up and I scorched some chaeto before learning to reduce my time and pull the light back as far as I could – about 8 inches above the water line. I have 10X flow in my sump but it still will not spin the chaeto to keep it from burning. Now the chaeto is thriving with 6 hours of light nightly and my nutrients are at near zero using Triton method.

  1. I just finished plumbing my fuge. Starting it up tomorrow. Once it’s cycled I’ll be adding chaeto and pods.

  2. I don’t have many copepod eaters in my reef, is it okay if there are an excess amount crawling on rocks/glass?

    1. greg.chernoff

      It is perfectly OK, and they are helping to keep your tank clean! Also, they are relatively self regulating, if there wasn’t enough food in the system you would undoubtedly have far less !

  3. brennanlottes

    My tank has been going through the algae cycle and your mocha ogo in my fuge is growing like crazy

    1. greg.chernoff

      Our 5,280 blend provides three great species that will help clean algae and detritus from your system, they make a great compliment to amphipods!

  4. Douglas Campbell

    Do you have to use a substrate? I have everything I need for the refugium except the macroalgae and substrate.

  5. Diana Aliprandi

    Great article. I am upgrading my tank to a 75 gallon which will have a sump. I am planning out to do a review gym after reading your article

  6. Kevin R Gravier

    I would love to have the space to put refugium on my biocube, definitely on a bucket list for my reef aquarium.

  7. I would like to set up a display refugium. Chaeto, does not look very attractive. Are there other effective algae’s that you would recommend that are also attractive?

  8. Kenneth Showman

    I am currently in the process of building my in sump refugium. Already have a Kessil H380 and some Marinepure bio cubes. Just need to get some macroalgae, pods, and phytoplankton to complete. After research and reading reviews, Algae Barn is the only site I’ll be ordering from. Love that you guys carry only the best high quality products, and give knowledge information to help people make the right choices.

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