What are the Best Substrates to Use for a Refugium?

Refugiums are a wonderful component to achieving a healthy and thriving reef tank. Refugiums serve as a haven for microfauna, microalgae growth, and other purposes depending on the goals and needs of the reefer and aquarium. Refugiums set up for filtration and microfauna typically contain some form of macroalgae and a substrate. There are many different substrates to choose from when choosing what to place at the bottom if anything of your refugium.

What are the best substrates to use for a refugium? The best substrates to use for a refugium include live sand, live rock, live rock rubble, Marine Pure blocks, Miracle Mud, or just leaving the refugium bare bottom.

In this article, I will detail the different substrates and some of the pros and cons of each. I will also share what I prefer to use in my refugium setups. Different reef tanks will have different needs and individual reef keepers will have different goals with their refugium so one size best substrate choice probably doesn’t fit, but knowing the options can help you dial in a best-fit decision. Knowing your specific tank needs and having a goal for your refugium will make a substrate choice easier.

Live Rock as Refugium Substrate

Live rock can be a great substrate to use in the bottom of your refugium. Live rock in the refugium gives additional space for helpful bacteria to populate and serves as a main nutrient exporter in the reef aquarium. Live rock can also house microfauna like copepods and amphipods. Micro fauna raises the biodiversity of the tank, can serve as a constant food source for fish and corals, and are excellent members of the reef clean-up crew. Using the porous rock you can find will give ample housing quarters for both beneficial bacteria and micro fauna populations. If you are using your refugium for macroalgae growth you can put a few larger flatter pieces on the bottom of the refugium preserving the majority of the sump for macroalgae growth. If you use larger pieces of live rock in your refugium and need to perform maintenance in your refugium, removing the live rock is simply done by taking it out and siphoning out any detritus build-up.

Live Rock Rubble

Live rock rubble is another option to consider for the refugium substrate. Live rock rubble is simply smaller pieces of live rock most of the time being in the ping pong ball or smaller size range. Live rock rubble has all the same benefits as live rock. In my opinion, it does have some added disadvantages though. I’ve experimented with live rock rubble and found that I get more detritus to build up with live rock rubble than with larger live rock pieces. Detritus seems to build up between the pieces and stay there until it is physically removed or it completely breaks down into dissolved organics going back into the water stream. It also takes a bit more effort to remove rubble from the refugium as there are more pieces and they are smaller. When cleaning the refugium in my sump with rubble, I would remove the chaeto, remove the rubble, shop vac the detritus, and replace the rubble and chaeto back into the sump. I usually need to do this about every quarter of a year to keep it from becoming a nitrate factory.

Live Sand as a Refugium Substrate

Live sand as a substrate is a bit of a controversy in the hobby. One camp feels that a deep sand bed can have denitrification effects while the other camp says that a sand bed is a nitrate factory. A deep sand bed is generally considered a sand bed 6” or greater with the typical setup being in the 6-8” range. Within a deep sand bed, there are potentially anaerobic zones with little oxygen. Bacteria in this area convert nitrate into nitrogen gas which then bubbles out of the aquarium thus removing nitrate.

The other school of thought is that sand beds in general collect waste and detritus and over time will collect too much making it a ticking time bomb waiting to go off leading to a catastrophic failure. There is probably validity to both sides of this discussion and I believe that the more important question is if you choose to go with a deep sand bed in the refugium, it will require additional maintenance including replacing the sand at some point. I like to have sand in my display tank for aesthetics, attempting to mirror nature and some of the tank inhabitants that I keep using the sand. With sand in the display, I generally do not keep sand as a substrate in the refugium. Deep sand beds are less common in the hobby these days.

Miracle Mud as a Refugium Substrate

Miracle mud is another product similar to live sand. The product claims to have the ability to help replenish essential trace elements in the reef tank while containing healthy bacteria to help with denitrification. There are a lot of examples where reef tanks thrive off this stuff in the refugium. Similar to sand this product also needs to be maintained regularly. Most people will remove a portion of existing mud and replace it a few times a year. It is usually not a large chore to swap out mud, but it can have built-up waste and loose efficacy if not regularly maintained over time. Cost is another factor in the product.

Marine Pure Blocks, Balls, and Plates as a Refugium Substrate

Marine pure blocks are another product that works similarly to live rock. Marine Pure blocks are a very porous material that creates massive amounts of surface space for helpful bacteria to populate. With the material being so porous it also allows for water to flow through the material. There are various forms of the Marine Pure including blocks, plates, and spheres. The product is very fragile and can be cut or shaped to fit in various parts of the sump including between baffles. There are reports of Aluminum leaching into aquariums from Marine Pure Blocks and it’s unknown if this is an issue for corals and livestock. There are plenty of thriving reef tanks with Marine Pure Blocks. Cost is another consideration with Marine Pure blocks.

Going Bare Bottom Refugium with no Substrate

Going bare bottom refugium is the ultimate minimalist approach. For those that want to only grow macroalgae, this is the perfect option. A bare bottom refugium is the simplest method to maintain. You simply siphon out the detritus when if it builds up. No substrate means little to no maintenance.

My Substrate Preference for the Refugium

My typical tank setup usually consists of live rock in the display tank, a medium stock of fish to gallons, and a mix of corals including SPS, LPS, and softies. My goal for refugium is to reduce nitrate and phosphate through the continuous growth of macroalgae, increase biodiversity with microfauna like copepods, and prevent detritus build-up in the sump.

With the needs of my tank known and refugium goals, I prefer to use live rock on the bottom. I look to choose live rock pieces that are flatter usually about the size of a medium pancake or so and can be spread across the base of the refugium with about a 1-2” gap between them. Having large rocks makes it easy to maintain the refugium when needed as I can simply remove the rocks and place them in a bucket of saltwater while I clean the fuge out. With a mix of bare bottom and larger rocks, I find that detritus build-up is rather minimal in the fuge as it moves better through the rest of the sump getting taken care of during other filtration stages. I also try to use the most pourest rock I can find to promote a living space for copepods and amphipods. Having just a few rock pieces in the refugium also maximizes the space to grow macroalgae. I prefer to use Chaetomorpha macroalgae and will often fill the fuge chamber with growth.

I don’t find the need to have the additional bacterial surface area Marine Pure blocks offer as I believe this is accomplished enough in the display tank’s live rock. I have tried live rock rubble in the past and found it to collect a lot of detritus and was harder to maintain with the individual little pieces. The same went for sand and miracle mud-type products, they just have the potential to trap waste and are harder to maintain when needed.

Any of the options are potentially good options for your refugium. Before choosing the right one for your aquarium you’ll want to establish a goal for your refugium and be willing to accept and perform the required maintenance that the different substrate options require.

Related Questions

What are Marine Pure blocks made of? From the company website, Marine Pure is made of an inert Aluminosilicate ceramic that is fired at over 1000 degrees to prevent leaching.

What is Miracle Mud made from? From the company website, Miracle Mud is 80% harvested from oceanic mud from deep waters and dried on land. The remaining 20% is a formulation of many minerals and trace elements.