The growth of microorganisms such as copepods, amphipods or macroalgae in your saltwater aquarium can be hard especially if you have a large or growing fish population. The microorganisms have no chance of thriving in an environment with a huge population of predators. Yet they are crucial if you want to create a natural habitat for your saltwater fish.

They serve as nutritious food for the fish and sustain the water quality in your aquarium. The absence of a hospitable habitat for microorganisms in a saltwater aquarium necessitates the need of a refugium.

But it isn’t just about creating a hospitable habitat for essential microorganisms, read on to discover numerous other ways a refugium can benefit your reef aquarium.

What is a Refugium?

It is important that your saltwater aquarium resembles the natural reef environment as much as possible. It is one way to ensure that there are adequate oxygen levels in the aquarium and that your fish enjoy a natural diet with little work on your part. That what happens in the oceans.

The fish feed on the microorganisms growing at the floor of the ocean. When the remains of what the fish eat fall to the reef, the microflora and microfauna on the reef use these remains as a source of nutrients and thrive delivering more live food to the fish. This simple natural cycle supports organic life in the seas and oceans.

If you want rich aquatic life in your aquarium, setting up a refugium next to your aquarium is among the best ways you can achieve that. A refugium imitates the natural habitat of fish right in your own home in a way that doesn’t take up too much space.

In a nutshell, a refugium is just a smaller aquarium you can use to cycle water in and out of your larger saltwater tank. A good refugium should have an aragonite live rock, a deep sandbed – or even a deep mud bed – and macroalgae. Food remains and waste from the fish falls to the sand or mud bed and the macroalgae use it as a source of the nutrient. In this way, the macroalgae flourish and become a source of live food for the fish. This is how a refugium creates a natural reef environment in a saltwater aquarium.

What’s the Difference Between a Sump and a Refugium?

It is important to understand the difference between a sump and refugium because while they are similar in some of their functions, they are fundamentally meant for different purposes. Sure, you can use both to cycle water in and out of your reef aquarium. Sure, they are connected the same way to the larger tank. And sure you may find a two in one refugium that also contains a sump and vice versa. But choosing a refugium instead of a sump or vice versa should depend on what you actually want to achieve.


The difference between a refugium and a sump is in what they are fundamentally meant to do. A sump is a container that collects water for filtration – it may contain filters and monitoring equipment – buts its core purpose is to collect water for filtration. In contrast, refugia are mainly used to promote the growth of microflora and microfauna that are essential in giving aquariums a natural reef environment.

While a refugium provides a heaven for microorganisms to thrive away from predator fish in the main tank, a sump alone cannot achieve that.

Refugium For Saltwater Aquarium

Benefits of Installing a Refugium

Without a refugium, it’s hard to maintain a natural aquatic environment in your saltwater aquarium. Consider this: you have a thriving fish population and you want to keep the population growing, how will essential microorganisms survive in the main tank if there’s a large predator population feeding on them all the time? You need a separate place where microorganisms can thrive while still supplying a generous amount of natural food to the fish. And a refugium is the easiest way to achieve that.

Read on to learn more about how a refugium can help you achieve an optimal natural habitat for your saltwater fish.

1. Controls Nitrate Levels

While nitrate is not as harmful to fish as ammonium or nitrite, it is still toxic. Sure the bacteria in your filter do a good job in turning highly toxic ammonium – which comes from fish waste and leftover food – into nitrite and then into nitrate which is less toxic. But at high levels, nitrate also creates an inhospitable environment for fish.

The easiest way to keep nitrate levels hospitable is to use a refugium. Because plants metabolize nitrate, the microflora in the deep sandbed of a refugium uses up excess nitrate in the aquarium making the aquarium hospitable for fish.

2. Gives Micro-crustaceans a Quality Habitat

CopepodsWhile you can maintain water quality in your saltwater aquarium by mechanical means – by, for instance, replacing the water in the tank with clean water – it is always a good idea to use natural means to maintain water quality. A refugium for saltwater aquarium is the best way to sustain water quality naturally. Micro-crustaceans (such as copepods) in a refugium help to keep the water in the aquarium system clean and habitable for fish by breaking down food remains and nuisance algae.

But without a refugium, it’s hard for microcrustaceans to thrive. They need a place to grow with minimum interference from predators. And that’s exactly what a refugium provides. In a refugium, these microorganisms can reproduce at an optimum range and reach enough numbers to keep food remains and excess algae in check.

3. Increases the Volume of the Aquarium System

The biggest challenge for any captive ecosystem is to ensure adequate oxygen levels at all times. Otherwise, the fish will suffer from insufficient oxygen and may not survive. And among the easiest ways to give your fish more breathing space is to increase the volume of water in circulation in the system.

It’s a case of the more the water volume, the higher the oxygen concentration. And if increasing the volume of water in your saltwater aquarium is your goal, then you should seriously consider setting up a refugium.

But a refugium doesn’t just give your fish more breathing space, it does more than that: it boosts the biodiversity in your aquarium system introducing a full range of zooplankton and phytoplankton. Consequently, the amount of oxygen and natural food available to the fish increases.

4. Sinks Sediments

Fish waste and food leftovers can be an annoying sight in an otherwise beautiful aquarium. Every aquarist wants their aquarium to be as clean and visually appealing as can be. In fact, that’s one of the major reasons for keeping an aquarium in the first place – for aesthetic purposes. If you want to keep the muck away, setting up a refugium is an excellent idea.

A refugium helps keep detritus away by making sediment sink to its sandbed. But how does it achieve this? Refugia have a rich diversity of zooplankton and phytoplankton, thus as the water cycles in the aquarium system, it moves considerably slower in the refugium. This slow movement of the water gives detritus enough time to settle at the bottom of the refugium so it doesn’t go back to the main tank, ensuring that your main tank remains as clean as possible. Thus it looks virtually appealing and your fish benefit from a clean habitat free of toxic waste.

5. Controls the Growth of Harmful Microalgae

When bad microalgae grow in a saltwater aquarium, they form an ugly film that is annoying to see. But that’s not the worst part. When the bad microalgae mature and die, they release all the nitrate they have back into the aquarium system, creating a toxic environment. But by growing good macroalgae in a refugium, you can control the growth of bad microalgae.

Good macroalgae take up the nutrients in the refugium sandbed leaving very little nutrients such that the bad microalgae cannot thrive. But the good macroalgae doesn’t stop there: it grows and shades the refugium bed and its own lower parts controlling not just its own growth, but also that of bad microalgae that try to grow. You can then harvest a mass of the good macroalgae and discard it or feed it to the fish. Controlling harmful microalgae keeps your aquarium beautiful and prevents the build-up of nitrate to toxic levels.

You will need lighting in your refugium for the optimum growth of macroalgae. Here is a good option for refugium lighting.

Your Saltwater Fish Deserve to be Happy and Healthy

Think about all the benefits that the inhabitants of your saltwater aquarium bring to your home. They reduce your stress levels. They give you a calming effect when you are anxious. And they keep you healthy by lowering your blood pressure. But that’s just the most notable benefits. Fish also boost productivity and can benefit you and your family in many other ways.

Considering all these benefits, the fish need to be healthy…and happy too. And as you have seen, you can keep your saltwater fish healthy and happy by setting up a refugium. A refugium prevents the build-up of nitrates to toxic levels, promotes the growth of essential microorganisms, sinks the muck in your aquarium and does more good that you will begin to see once you have connected it to your aquarium system.

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