What is a Refugium Aquarium?

As a beginner fish tank owner, you might be so focused on the basics that you’re yet to learn about refugia.

As a reasonably seasoned fishkeeper, you may be relying on aquarium extensions to do things they can’t do, or worse—installing the wrong type for your needs.

Like many aspects of this hobby, refugia are extremely useful yet not fully understood.

In this article, we look at all things refugia, including when, why, and how you should use them.

What Is a Refugium?

A refugium is a place of refuge.

Depending on your aquarium interests, it may provide protection for targeted plants (usually macroalgae) or animals (especially copepods).

Many delicate species benefit from a refugium as it keeps them separate from larger fish in the main tank.

The refugium may also serve functional purposes such as water filtration, which we take a closer look at further along in the article.

Aquarists need to understand which practical purposes refugia provide to avoid misusing them.

How Does a Refugium Work?

A refugium works by creating a segmented compartment away from the rest of the fish tank.

In this area, several types of filtration occur to create a healthy, natural environment for the aquarium:

  • Animal filtration
  • Vegetable filtration
  • Mineral filtration

Animal Filtration

When debris and uneaten food settle at the bottom of the refugium, microcrustaceans, such as copepods, feed on them.

The process effectively maintains water quality and allows microcrustaceans to multiply.

They serve as a natural food source for fish in the main tank.

Vegetable Filtration

Macroalgae that’s grown above the rock and sand utilizes nutrients in the water.

The process maintains the proper nutrient levels and may reduce the number of water changes that are required.

There are some exceptions to macroalgae’s ability to maintain water quality. Some species of Caulerpa can cause cloudy water while in the sexual stage of their life cycle.

You can solve the problem by illuminating the refugium 24/7 and pruning to prevent Caulerpa from reaching their sexual stage.

A refugium should be illuminated on a lighting schedule opposite the main aquarium to provide oxygen during nighttime hours. Doing so reduces nighttime pH fluctuations.

Mineral Filtration

You may use a deep sand bed (DSB) to promote the growth of beneficial bacteria in the refugium.

The bacteria in the sand perform natural nitrate reduction to maintain water quality. You may want to add some animals, such as worms and snails, to help stir the substrate.

A stack of additional live rock is an excellent alternative to sand.

It is beneficial if you need more filtration capacity but lacks enough room in the display tank. The rocks improve water quality and encourage copepods to grow and microfauna to feed fish in the display tank.

What Are the Benefits of a Refugium?

There’s a lot of stuff going on in a refugium. The natural processes that unfold are undoubtedly exciting, but you may wonder whether the cost of installing an additional compartment is worth it.

There are six significant benefits of installing a refugium to your aquarium, and we discuss each below.

Nitrate Control

The deep sand bed in a refugium hosts anaerobic bacteria that metabolize nitrate.

Denitrifying bacteria and purple non-sulfur bacteria work together to purify water naturally. The process decreases the frequency of water changes that are needed.

Algae Growth Control

Microalgae take up nitrate as they grow. The process eliminates “bad” microalgae that form unsightly films and turfs in fish tank water.

The “good” algae can also be harvested and discarded, or if palatable, fed to herbivorous fish in the main tank.

Food Growth

In addition to maintaining good water quality, microalgae in refugia provide habitat for microcrustaceans such as copepods.

Pods feed on decaying microalgae and, with the perfect living conditions, produce at a rapid rate. The process increases biodiversity in the tank and provides food for other fish.

Sediment Pooling

We’d all rather not have organic debris anywhere in the aquarium, ut, seeing as it’s unavoidable, it’s better off in the refugium than in the main tank.

A heavily planted refugium acts as a sediment sink and prevents organic detritus from accumulating in the main tank.

As the water currents pass through the dense patch of weeds, they slow down and allow organic matter to settle at the bottom of the refugium.

Microcrustaceans feed on the detritus and make for a neat in-water waste disposal system.

Water Volume Gain

By adding the water holding capacity of your aquarium system, you’re giving your fish more room to move around and breathe.

Besides, you’re diversifying the ecosystem.

Unlike a sump, which is essentially a dead space for compartmentalizing filtration equipment, a refugium is a hotspot of biological activity.


Refugia can be esthetically pleasing aquaria that elevate the appearance of the whole system.

You may display your refugium in a tank beside your primary display and use a gravity drain to carry water to the lower tank. Use a pump to move it back to the higher tank.

For esthetic purposes, you could have a refugium consisting of seagrass on top of the dep sand bad.

A growing mangrove plant and corals may further improve the appearance of the compartment.

What Are the Types of Refugia?

A refugium can be incorporated above, below, along the side, or inside the aquarium to serve different purposes.

Separate Tank or In Sump Refugium

This is a stand-alone refugium set up above, below, or next to the display aquarium.

A below-aquarium refugium is the most common and works in the same manner as a sump.


  • Costs the least out of the different types available—if you use a plain tank and simple technology.
  • Is kept under wraps, so you don’t have to worry about esthetics.
  • Can hold the protein skimmers.


  • You may forget to check on your critters.
  • Can be expensive if you opt for high-tech options.

In-Tank Refugium

This is a small box attached to the inside wall of your main tank.

It lets water in and out while keeping critters in and big fish out. It may also be built using sheets of glass to partition part of the aquarium.


  • Doesn’t take up any more space
  • Gives satisfaction of observing critter activity and growth
  • Cheaper than a hang-on refugium


  • Doesn’t add water volume to the tank
  • May not be esthetically pleasing
  • Can’t run separate lighting schedules from the aquarium

Hang-on Refugium

This is a separate container that hangs on the outside of the main tank.

It’s typically attached to the back of the aquarium and uses an extra pump to move water in and out of it.


  • Adds water volume to the system
  • Cheaper than a high-tech sump


  • Can’t be too big or heavy since it’s hanging on the tank
  • Requires more space—may not work if your tank is too close to the wall
  • Can be hard to clean
  • More expensive than an in-tank option

Refugium Tips and Guidelines

Here are some tips for you in case you want to keep a refugium aquarium:


One of the primary uses of a refugium is to house delicate species.

It’s beneficial for small inhabitants like brine shrimp and copepods that fish would otherwise eat in the tank before they’re of the proper size.

Water Flow Rate

The optimal water flow rate depends on what you’re using the refugium for.

If you’re culturing algae, then you need a faster flow to make it tumble. If you’re housing a DSB, you need a slow flow to avoid stirring up mud and carrying it into the main tank.

Before installing a refugium, research its needs and choose pumps accordingly.

It’s advisable to separate the refugium from the tank to have a dedicated pump that carries water at the proper flow rate.


If you’re running a basic DSB, no light is needed. However, if your refugium has photosynthetic organisms such as algae, then you need light.

Depending on the species of algae, you may have to keep lights on 24/7, alternating with those of the main tank.

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