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How to Set up a Refugium: The Complete Guide

Refugiums seem like a new trend in marine fishkeeping but they have actually been around for decades. They provide space for bacteria, macroalgae, and invertebrates to further break down and assimilate organic and inorganic matter from the main aquarium.

And in doing so they help control the growth of nuisance algae, prevent the buildup of nitrates, and even provide a handy food source for your display animals. Let’s take some time to understand why refugiums are so useful for marine hobbyists!

Why Should I Set Up a Refugium?

Wondering if setting up a refugium is worth the hassle? Here are a few reason why we recommend giving it a shot:

Nutrient Export & Complete De-Nitrification

One of the main functions of a refugium is locking away free-floating nutrients. These compounds and elements include nitrates, phosphorus, and organic debris and detritus.

In a more traditional setup a protein skimmer would account at least for organic molecules by foaming and removing them. This also prevents nitrate buildup since the organics don’t decay into ammonia and nitrite via bacterial action.

In a refugium, a more ecologically minded approach is taken. Organic matter is allowed to go through the normal phases of breakdown into ammonia, nitrite, and nitrate (the main steps of the Nitrogen Cycle).

Emoody26 at English Wikipedia / CC BY

Nitrate is the final product and is the least toxic of the three nitrogenous waste products. However marine organisms tend to be rather sensitive to nitrate compared to their freshwater cousins, especially marine invertebrates like corals and shrimp. Even low levels that wouldn’t affect fish can cause them stress.

Unfortunately most aquariums can’t support robust colonies of denitrifying bacteria because they are obligate anaerobes. This means that they are actively poisoned by the oxygen we take for granted as necessary for Life!

In a typical aquarium filter and substrate, there aren’t pores small enough to block water flow and allow anaerobic micro pockets to form. Fortunately in a refugium, by using the right substrate, we can create hotbeds for denitrifying bacteria to prosper.

Nitrate and phosphate are also important algal nutrients. In the majority of home reef ecosystems, problem types of algae like Brown (diatomaceous) and Coralline Algae are the only organisms that take up these elements. Nuisance algae can become unsightly growths coating your rocks, glass, equipment, and even your desirable corals, cutting them off from light and current.

A major benefit of a refugium is providing competition to unsightly algae by culturing beneficial macroalgae! Several species are incredibly easy to grow and by sucking up nitrates and phosphates they prevent problem algae from growing unchecked in the main aquarium.

Refugiums also provide a more comfortable home for the occasionally unsightly but essential members of your saltwater cleanup crew! Snails, hermit crabs, and brittle starfish will be much happier in a refugium.

Increased Biodiversity & Food Supply

brine shrimp

Live food sources are the best for fish in terms of quality and stimulation. However they aren’t always easy to source and are rarely convenient to keep on hand for future feeding.

Refugiums provide a separate compartment where you can cultivate organisms that would be quickly eaten in the main aquarium. Copepods, amphipods, and other tiny crustaceans favored by picky eaters like Mandarinfish can’t breed fast enough in all but the largest of reef setups.

However in your refugium you can provide a peaceful environment with lush macroalgae and a rich substrate for them to feed from. Occasionally they will get pumped into the main aquarium but they can also be harvested so long as you keep tabs on their reproduction rates.

Your macroalgae is another important source of food. Omnivorous grazers like Angelfish and dedicated vegetarians like Tangs & Surgeonfish require high-quality plant matter in their diet. Failure to provide it results in nutritional deficiencies like Hole in the Head (Lateral Line Disease).

Since refugium macroalgae grows so aggressively, some of the trimmings should be offered to any algae-eating fish for a balanced diet.

Water Quality Buffer

Whenever someone asks me how large of an aquarium they should buy my answer is always “the largest you can afford and have space for.”

The reasoning behind this is very simple: larger aquariums have more water. And the more water you have, the more breathing room you have if a problem arises in water quality.

A fish that wedges itself behind a rock before dying is a much bigger problem in a 10 gallon nano-reef than in a 55 gallon reef tank. Ammonia toxicity rises far faster. Nano tanks are much more quickly impacted by ammonia spikes from rotting organic matter, temperature swings, overdosing medications, and other issues.

By adding a refugium the volume of the secondary sump or tank adds to the total volume of the aquarium ecosystem! A 55 gallon setup with a 15 gallon refugium has 70 gallons of water capacity.

This may or may not allow you to keep more fish and invertebrates as well. On the one hand, you are providing both more water and more biological filtration to compensate for the increased load.

On the other hand the living space of your main aquarium is unchanged. Fish and invertebrates still need territories and room to grow, so whether you can safely keep more fish or not with a refugium is debatable.

Do be aware this applies only to under the tank-style refugium/sump systems. There are also hang on the side refugiums that are more like traditional power filters in terms of size. These don’t boost tank volume by very much but still provide all of the biological filtration benefits!

Another unexpected benefit to refugiums is added pH stabilization when carefully planned. If you already have macroalgae living in your main aquarium, you probably know that like all photosynthesizing organisms, they create oxygen during the day.

However what’s less well known is that at night, plants and algae actually use oxygen and release CO2. While this rarely adds up to fatal suffocation for fish, CO2 is mildly acidic, and enough can cause problematic shifts in pH.

By alternating your day-night light cycle with your refugium, you can buffer the O2-CO2 swing. When the main aquarium is on a day cycle, the refugium should be dark, and vice versa, to keep carbon dioxide and pH levels constant.

If you’re less concerned with stabilizing CO2 many aquarists run their refugium on extended or even 24/7 light schedules. This provides maximum macroalgae growth, nutrient uptake, and oxygenation.

Protein Skimmers vs Refugiums

Protein skimmers are a second, popular choice for organic waste control. While they operate by very different means both are worthy of consideration.

aquarium protein skimmer

Main Benefits of Protein Skimmers:

  • Removal of organics before they can decay into ammonia and other compounds
  • Better for organisms that require ultrapure water conditions
  • Less space required
  • Mechanical filtration can be more convenient and easier to manage vs a secondary ecosystem

Main Benefits of Refugiums:

  • Allows for the full detoxification of nitrate into nitrogen gas through anaerobic action (with the right substrate)
  • Provides space for detritivores and macroalgae to grow, which can be used as food
  • Macroalgae oxygenate the water and prevent nuisance algae growth
  • Can be a significant increase in overall aquarium volume (like a sump)

It doesn’t need to be an either-or decision, however, because there are advantages to using both systems. Many aquarists use sump systems designed to provide space for both protein skimmers and refugiums.

You’ll need to give some thought as to the purpose of each, as the skimmer, by removing organics, could cause problems for your refugium detritivores. However macroalgae would still thrive on excess nitrates and phosphates!

Refugium Lighting

While algae are famously tolerant of low light conditions you’ll want to provide the right spectrum to fuel rapid growth. I recommend choosing spectrums ideal for green macroalgae species since they grow faster than most red macroalgae varieties.

Refugiums are so popular nowadays that you can pick up LED light strips with spectrums tailored to their ideal growth! One example is Innovative Marine’s ChaetoMax LED light strips. The name is a clue to their purpose in growing beneficial Chaetomorpha macroalgae, a popular and prolific refugium species.

Innovative Marine ChaetoMax Refugium LED Light (9 Watt)
  • Designed for Sumps and AIO Aquariums. Fits all...
  • 45 x 0.2W 60mA LEDs: 5 - 420nm BLUE. 10- 470nm...
  • Small form factor (DIMS: 6.7” x 1.85” x...

Refugium Substrates

Refugium substrates should be carefully chosen because the added surface area provides living space for detritivores and microorganisms. Sand is the usual choice as you can have an immense surface area thanks to the tiny grain size. However refugium mud, rich in silt, is by far the best choice.

Carib Sea ACS00526 Mineral Mud Filter Media for Aquarium, 1-Gallon
  • Refugium substrate for marine and reef aquariums
  • Provides the benefits of mud without the mess
  • A unique blend of sediments that duplicate...

Sand substrates require a greater depth (4+ inches) to create anaerobic zones for denitrifying bacteria to thrive. Thanks to the even smaller grain sizes in mud you can have denitrifying colonies with as little as 2 inches of refugium mud.

Keep in mind that adding sand stirrers like Brittle Starfish will cause problems for your anaerobes since they constantly aerate the sand with their burrowing.

Biodiversity for Your Refugium

Here are some of the different plant & animal species that you can add to a refugium:

Refugium Plants & Algae


Macroalgae are the most important additions to your refugium. Thanks to their rapid growth they can soak up nitrate and phosphates that can then be removed from the system entirely through pruning.

Macroalgae are also valuable food for plant-eating fish and invertebrates. And if you’re so inclined, many species like Sea Grapes (Caulerpa racemosa) and Sea Lettuce (Ulva lactuca) can be eaten by humans as well.

So long as you provide a constant flow of water for CO2 and nutrients and lighting of the proper spectrum, macroalgae form a hardy, functional core to any refugium setup.

Mangrove Trees

Mangrove trees are extraordinary trees that grow in tidal marshes around the world. They are a keystone species in ecology, one that has a disproportionately large impact on the environment.

They are becoming more popular in the trade because they can be grown in marine refugiums. But in all honesty, Mangroves are more of an interesting novelty. They grow much too slowly to export nutrients well compared to macroalgae. They need full-spectrum lighting and either a rich sand substrate or refugium mud.

And lastly, they are trees, and will grow enormous. If you have skill in bonsai cultivation you may be able to control their growth, otherwise your Mangrove seedlings will eventually need transplanting.

Still, if you’re fascinated by them and want diversity for your refugium, consider picking up some Mangrove seed pods or seedlings!

Refugium Animals

Tiny Crustaceans

Small crustaceans are some of the best organisms to culture in a refugium. Copepods, amphipods, mysid shrimp, and other small critters are some of the most popular food sources for marine fish.

It’s all but impossible to grow them in the main aquarium because they won’t be able to reproduce fast enough before being eliminated or filtered out. However in a refugium a few will get pumped into the main system on occasion, providing a tasty treat for alert fish.

If your refugium is large and mature enough you can even cultivate large numbers of them for semi-regular feedings.

Hermit Crabs

Hermit Crabs provide tons of benefits and at least a few should be kept in the main aquarium. They not only eat detritus but also nuisance algae. However if algae starts to run out due to your refugium macroalgae outcompeting it consider moving them to the refugium! There the crabs can still eat detritus but now have a never-ending salad forest to live in!


Brittle Starfish are detritivores that often find a place in the marine aquarist’s saltwater cleanup crew. Nocturnal and rather fast for starfish, they find leftover food in the deepest crevices thanks to their sharp sense of smell and thin, grasping arms.

While they do well in the main tank they can be kept in the refugium as well. Be aware that brittle starfish are something of a top predator there and will also eat the worms and small crustaceans that call the refugium home.

A refugium is one of the few places Asterina starfish can live without being a terrible problem. Asterina can reproduce by breaking themselves into pieces and can completely overwhelm an aquarium in a short time.

However there are specialist predators like Harlequin Shrimp, which eat only starfish. A reserve supply of Asterina in your refugium will provide a never-ending food supply for them.

Fish and other Animals

A refugium can even provide a quasi-quarantine tank for fish and invertebrates. Since the water flows into the main aquarium it won’t isolate them from spreading diseases. But if an animal gets an open wound, needs to be separated due to behavioral issues, or has trouble feeding, a refugium provides an ideal hospital zone for recovery.


Biological filtration methods tend to be a bit more complex and research-intensive. However few are as rewarding as refugiums. Not only do they help maintain pristine water quality but they even act as a secondary ecosystem that’s just as interesting as your main aquarium!

Jason Roberts
About Jason Roberts
Jason is an aquarium fanatic that has been a fish hobbyist for almost three decades.

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