If your first fish tank was anything like mine, all you needed to worry about for substrate was which color rock you'd like covering your undergravel filter.

For the record, I chose blue and black.

A few decades (and many fish tanks) later, the aquarium hobby has made great advances in understanding substrate. Unfortunately, too many hobbyists still approach substrate as an afterthought. While substrate choice might not make the difference between success and failure in the marine aquarium hobby, choosing the right substrate for your system can certainly make a big difference. This article will cover the most popular choices today along with some of the reasons they are employed.

Surprisingly, substrate has been a contentious issue among hobbyists for some time. For years, flame wars have spread like wildfire in popular internet message boards with reefers insisting their method is best. I have no interest in reigniting this argument. It is, after all, just sand we're talking about. I believe there are many ways to succeed in keeping aquaria. Please also keep in mind that the purpose of this article is to be broad and helpful without getting too technical. My desire is to provide you, the reader, with the tools necessary to make the best decisions for your dream system, be it a jawfish jungle gym or palace of chalice.

Over the years, different trends have swept through the hobby, gathering acolytes and protesters alike. At different times in the hobby, shallow sand beds, deep sand beds, fake sand beds, bare bottom systems and mud refugiums have each been all the rage. Thanks to these changing trends, the hobby now has a wealth of information available on the value of different substrate methods.

Bare bottom tanks were all the rage for a few years and are still a popular choice. Instead of mulling over which sand to use, many hobbyists decide not to have any sand at all. Some leave the bare glass/acrylic showing to be covered in coralline algae over time. Others use starboard (cutting board material) as a bottom material to be coated over time. I have even seen hobbyists create fake sand beds (FSB) by epoxying a thin sheet of sand to the cutting board material. Fake sand beds eventually get covered by coralline and end up looking very similar to a bare bottom system with a bit more texture.

High flow systems that demand low nutrient levels, like SPS dominant tanks, are frequently run bare bottom. There are several advantages to this approach. High flow promotes stony coral health while keeping wastes suspended in the water for removal. This level of flow does not mix well with fine sand and can create sandstorms inside the display. Wastes that do manage to settle are easily siphoned out during water changes. Another benefit to forgoing sand is the need for fewer "janitor" organisms, like nassarius snails. Having a bare bottom sump makes for easy waste removal although I prefer the use of some kind of substrate for a refugium.

While going bare bottom seems like a natural choice for a stony coral system, there are some drawbacks. Most important—to me anyway—is the unnatural appearance. To my eye, the positive/negative space contrast between the rockwork and substrate makes for a more visually appealing display. Without sand, there are several burrowing species that will not adjust to (let alone thrive in) the system. Removing substrate from the equation also removes the beneficial filtration (nitrifying and denitrifying) and buffering (release of calcium, carbonates, etc. from the dissolution of aragonite) that sand can provide.

Enough about bare bottoms. Let's talk about the beach.

Most reef hobbyists choose shallow sand beds (up to 1") for their display aquariums for a variety of reasons. Shallow sand beds seem "natural" to most hobbyists and have a lot of value. Aesthetically, you simply cannot duplicate the organic way sand looks in an aquarium, regardless of how you doctor up the bottom. No matter how stunning a bare bottom system may be, I feel they always appear to be missing something.

Having a sand bed means being able to keep a wider variety of fish. Waste is fairly easy to siphon out of a shallow sand bed. Shallow beds also provide additional nitrifying filtration (conversion of ammonia and nitrite into nitrate). Some buffering will also occur from the shallow bed as the aragonite sand slowly dissolves. It is unlikely this will be enough to prevent the need to dose but may contribute to more stable water parameters. For a refugium or sump, a shallow sand bed provides very little benefit and is not recommended.

For all their popularity, shallow sand beds can be a pain. Anyone who has witnessed a running powerhead fall onto the sand bed and watched their precious corals disappear can attest to that. Plus, over time the sand bed dissolves. This means it will need to be replaced, which is not a fun chore. Shallow sand beds provide some biological filtration and buffering, but not enough to make a significant difference in an otherwise well-designed system. This is not to say that a shallow sand bed doesn't have value, because it does. In my opinion, its primary value is what it contributes visually to the display and to the happiness of its inhabitants.

Now that we've covered the surface, let's get deep.

Most hobbyists define a deep sand bed as having a substrate depth of at least 3 inches (many reach 6+ inches). If you think about it, this is the most "natural" approach. When was the last time you were digging at the beach and had to stop after 1 inch because there was no more sand?

Greater depth allows for multiple zones, providing greater biodiversity and better filtration. Towards the surface, nitrifying bacteria and benthic sand-sifting organisms like brittle stars, snails and copepods can be found gobbling up settled waste. As these organisms sift through the sand, nutrients migrate to the lower layers. These deeper zones harbor denitrifying bacteria that convert nitrate into nitrogen, completing the nitrogen cycle. This is perhaps the single best reason to employ a deep sand bed and why they are frequently found inside refugiums.

Not everything in a deep sand bed smells like roses. Deep beds can harbor reducing bacteria capable of producing toxic sulfides responsible for that rotten egg smell you may have encountered. Poorly maintained sand beds can easily become nutrient sinkholes. Many reefers also fear the dreaded "old tank syndrome," frequently attributed to deep sand bed systems running for several years. While there is vigorous debate in the hobby on the existence of such a syndrome, it is possible that a poorly designed or maintained system can become a storehouse for toxins and nutrients that turn into a ticking time bomb. Removing or replacing a deep bed can be a logistical nightmare and dangerous to the system's inhabitants. Oolitic "sugar size" sand, which has the high surface area perfect for a deep bed, is prone to being stirred up by pesky gobies and wayward flow.

The last "system" I would like to cover is mud substrate. Originally made popular by Leng Sy, it is rarely used in a display tank (except to create specialized biotopes) but sometimes used in a refugium. A mud substrate is usually 1-2 inches deep and used as a bed to grow a macroalgae like Caulerpa. Rubble rock placed in the system is occasionally used as a breeding ground for copepods and other small critters. The mud acts as a biological filter and, over time, releases trace elements into the system to be used by coral. This also has positive effects on fish, as it is reported to reduce issues with head and lateral line erosion (HLLE). Mud substrate refugiums help create stability through nutrient export, release of trace elements and minimized pH swings.

Hobbyists that use mud beds swear by them but they are not as popular as they once were. The use of Caulerpa for nutrient export has also declined. Aquarium-cultured Caulerpa is so hardy it has become an invasive species in areas where it has been introduced, decimating entire sections of reef. Chaetomorpha, which has quickly replaced the use of Caulerpa, needs no bed to grow and doesn't appear to have the same harmful side effects. Half of the mud needs to be changed annually, which can be a bit of a chore. The denitrifying properties of a deep sand bed are also lost.

There are several options to consider when choosing a substrate. While mud is usually similar in consistency between manufacturers, sand is rated by grain. Fine "sugar size" sand will have grains no larger than 1mm. The small grain size provides the most surface area for filtration but is easily disturbed. Medium grain sand, like special-grade reef sand from CaribSea, will be up to 2mm. medium grain sands provide a balance of surface area for filtration and are less likely to get disturbed. Larger grain sands like crushed coral include anything larger than 2mm. Large sized sands tend to collect a lot of waste, but are excellent for burrowers when combined with smaller sands. Sands can also be broken down into aragonite (calcium carbonate-based) and non-calcium carbonate. Aragonite has the advantage of dissolving over time into calcium and carbonate ions providing additional support for coral health.

There are also more novel ways to use substrate. Anthony Calfo's remote deep sand bed (RDSB) concept, where a simple 5 gallon bucket is filled with sugar sand and filtered water is slowly run over the surface. The result is an efficient and inexpensive denitrator. I have seen top-off water passed through an aragonite chamber to buffer the incoming water. I have run this setup myself using RO canisters with modest results (RO water working much better than RO/DI). Many hobbyists are also starting to make their own aragocrete "live rock," for which several recipes and techniques exist.

So which method(s) are right for you?

I recommend carefully planning your new aquarium system before getting started. Take into consideration the feeding and environmental requirements of your proposed tank's inhabitants. Will fish be present that require substrate to survive? Will the corals you intend to keep thrive in the nutrient levels of your system? How difficult will the system be to maintain?

Most of my current preferences and practices are a result of learning from mistakes myself and others have made. I use a shallow sand bed in my display for wrasses and shrimp gobies. My sump is bare bottom to ease detritus removal during water changes. I maintain a deep sand bed in my refugium to assist in nitrate removal and buffering.

I suggest researching what has made other aquarium systems successful as you plan your own. There is a wealth of knowledge available in our forum and knowledgebase. And, of course, you're welcome to contact us at any time for assistance. We'll share our experience with you and offer you personalized recommendations based on your goals and equipment.