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Related FAQs: Marine Substrates, Marine Substrates 2, Marine Substrates 3, Marine Substrates 4, Marine Substrates 5, Marine Substrates 6, Marine Substrates 7, Marine Substrates 8, Marine Substrates 9, Deep Sand Beds, Refugium Substrates/DSBs, Live Sand, Mud Filtration 1Plenums, Nitrates, Sand SiftersAquascapingCalcium, FAQs 1, By Type: Aragonite/s, Coral Sands, Silicates, Dolomites/TapAShell, Southdown & Such, Collecting Your Own, & Physical Make-up, Size/Grade, Location, Depth, Marine Substrate Cleaning 1, Marine Substrate Cleaning 2, Moving/Replacing/Adding To, Marine Substrate Moving/Replacing/Adding To 2, Substrate Anomalies/Trouble-Fixing,

Related Articles: Marine System Substrates (Gravels, Sands) by Bob Fenner, Marine System Components, Deep Sand Beds, Plenums, Live Rock, Biofiltration, Denitrification, Live SandSand Sifters

Choosing a Substrate
for Your Marine Aquarium


Sara Mavinkurve  

One of the most important decisions marine aquarists make before setting up a new aquarium is what substrate to use (or if they will use substrate at all).  This article is an introduction and overview of the most popular choices aquarists make, the pros and cons of each, and what you should think about before deciding what you want for your system. 

Points to Consider

The subject of substrate choice has been met with a lot of heated debate amongst marine aquarists, causing many aquarists to feel very strongly about deep sand beds (DSB) verses bare bottoms (BB).   Friendships have been tested, hearts broken, cyber wars waged!  Well, not to get too melodramatic, but it's been a hot topic to say the least.    Before you get caught up in the 'politics' of the matter, think about what you personally want.  What looks good to you?  What purpose do you want your substrate to serve?  Will it be a habitat for life?  Will it be an additional source of filtration?  Will it server an aesthetic purpose?  Then there are the practical questions.  Do you want something easy and low maintenance or do you enjoy spending a lot of time with your aquarium?  How big is the system you are planning?  What kind of animals do you plan to keep?  One should consider all these questions before deciding on a substrate.   As you'll read below, each choice has its advantages and disadvantages.

But before I begin this discussion of pros and cons of different substrates, I want to point out that, in my opinion/observations, there are three basic types of points that tend to influence the decisions we make and opinions we form about our aquariums and the world in general.  There's experimental evidence, anecdotal (or empirical) evidence and theory.   Aquarium keeping can be extremely frustrating in that what we might expect to happen theoretically doesn't seem to happen actually or experimentally (and vice versa).    Then there are always those anecdotal experiences we have as aquarists for which we have no explanation at all and appear to happen only to us.  Thoroughly discussing all points made in science, theory and/or anecdote on marine aquarium substrate choice could easily fill a book.  Since I'm limited here to a few thousand words, I can only give you a cursory review of these topics and hope that by the end of it I've sparked your interest and inspired you to do your own further research and reading.

Bare Bottom

Bare Bottom Advantages:

We'll start with the simplest choice: no substrate.  There are a lot of potential advantages to a bare bottom tank.  Firstly, they are low maintenance in comparison to substrate containing systems.  It's always convenient to be able to simply siphon up debris with every water change.  Secondly, for reef or coral containing systems, it's easier to get intense water flow without having to worry about 'sand storms' or piles of substrate gathering in one corner of the tank.   Corals can suffer significantly from sediment damage.  This happens in aquariums when sand lands on or rubs against the delicate soft tissue of any coral.  Not having to worry about this problem alone is incentive enough for many reef aquarists to forego the use of substrate altogether (especially for many SPS coral keepers who've been dying to try out a 5HP Pacer SE2JL HYC supplied surge device if only they could get the building permit).

Bare Bottom Disadvantages:

The disadvantage of a bare bottom system is that you won't have the additional niches for life that substrates add to a marine aquarium.  You won't be able to keep any animals that require a substrate to bury and/or borrow in.  In short, anything that you might gain from having a sand bed (or other substrate), you won't have in a bare bottom tank.  Aesthetically, some people find bare bottom tanks visually unappealing.  This writer disagrees with this last contention.  There are some fun things you can do with a bare bottom tank to make it just as visually exciting (or even more so) as any tank with a sand bed.  Use of starboard is one option.  An even more intriguing look is to grow soft corals along the bottom.  A 'carpet' of star polyps, xenia, and/or zoanthids can look very cool at the bottom of a reef tank.   Having a hefty population of soft coral polyps along the bottom of the tank might even provide some help with the 'clean up' of uneaten food and fish waste.  


There are several different ways to use sand as a marine aquarium substrate, but I'll focus on the few most common ways.

Deep Sand Bed

Defining 'DSB'

Before we can discuss deep sand beds, we have to define the term.  Though the very definition of 'Deep Sand Bed' can be a hotly debated issue in and of itself, I'm going to give it what I perceive as the most common and practical definition.  Commonly understood, a DSB is any layer of sand three or more inches deep, with a grain size no larger than 'sugar fine.'  If the grains of sand are much larger than granules of sugar, you're starting to get into 'crushed coral' or 'crushed aragonite' substrates that don't quite function the same way as finer grained substrates.  

The Nitrogen Cycle Refresher Course

In essence, the Nitrogen Cycle is the infinitely complicated path, set of paths, overlapping and diverging paths, twisted and sinister paths, etc. by which Nitrogen circles around and through the earth, air and water.   Thank goodness we don't need to know all that much about it.   I painfully recall, and perhaps some readers of this article do too, being required to memorize the basics of the Nitrogen Cycle in school.   I can also remember rolling my eyes thinking 'when am I ever going to need to know this?'   Huh, well, believe it or not, here it is again.  The breakdown of nitrogenous wastes (largely from animals), occurs via the Nitrogen Cycle.  This is not unique to aquariums.  I'm sure any self-respecting farmer could tell you just as much or more about the in-soil manifestation of the Nitrogen Cycle as any DSB-loving reef aquarist could tell you about the in-aquarium manifestation of this process.   Grossly over-simplified,  it's the pathways by which:

1)      Ammonia is fixed (by nitrogen fixing bacteria) to make Ammonium. 

2)      Ammonium is converted into nitrogen oxides (nitrites and nitrates) by nitrifying bacteria. 

3)      Nitrogen oxides are converted into nitrogen gas and water.

Aerobic bacteria accomplish the first two steps.  Anaerobic bacteria accomplish the third.  Anaerobic bacteria absolutely need an oxygen depleted space in order to live and do their thing.  In a DSB, the goal is to have the top layer be aerobic (containing oxygen), with oxygen concentration gradually declining to zero down into the sand bed.   In this way, a DSB can become an excellent natural filter.  Essentially, all biological aquarium filters work this way (with an aerobic zone in juxtaposition to an anaerobic zone).   However, in all such filters, the biological filtration capacity is limited by the surface area available for bacterial colonization.  In a DSB, this surface area is truly immense.  If you do the math, the surface area can get up to an acre or more in the average DSB!   

Of course, as with any over-simplification of a biological process, I'm leaving out countless side reactions and other by products.  For example, hydrogen sulfide is a significant by product of denitrification which is toxic to fish if it doesn't exit the system in the form of gas (which it is at room temperature).  When hydrogen sulfide precipitates iron sulfides, this is what turns areas of sand substrate black.  This phenomenon is why some zealous bare bottom advocates call DSBs 'ticking time bombs.'  According to the ticking time bomb theory, the anaerobic layer of sand in a DSB accumulates toxins and will eventually 'erupt' in a sudden cataclysmic release of a myriad of denitrification by products (such as hydrogen sulfide), causing a total tank 'crash' (sudden death of all live stock).   While I suppose it's possible for such a thing to happen, I doubt that it often does.   For one thing, as mentioned, hydrogen sulfide is a gas.  Thus, so long as the DSB is well populated with benthic organisms and the aquarium system employs good circulation and gas exchange, hydrogen sulfide should bubble out along with nitrogen gas and carbon dioxide, etc.  More poignant for myself personally, I had an experience with one of my own systems that caused me to seriously question the DSB time bomb idea. 


ANECDOTE: The following is a mere anecdote and should not be taken more or less seriously than any other anecdote.  I once had the good fortune of watching my 65g aquarium start to leak along the bottom rim.  It started as a drip, then a steady stream.  Well, you know how this goes.  In less than an hour, I was forced to drain the tank (water, sand and all).  I'm embarrassed to admit that I was terribly unprepared for such an undertaking and did not have nearly enough pre-mixed water or anywhere for the livestock to go except a few empty aquariums of various sizes and plenty of spare Maxi Jet power heads.   When I got down to my DSB (about 4 inches deep), I started to scoop it out in 20oz slushy-cup-fulls at a time.  The rotten egg smell was room-filling and noxious.  The sand just an inch or two below the surface was black.  There was every sign that at least parts of my DSB had turned into an all-out hydrogen sulfide toxic waste dump.  How long it had been this way, I don't know.   Regardless, all my fish, corals and invertebrates had no choice but to sit in that same water and sand for at least 3 days before I could replace the leak tank.  And yet, nothing died.  Of course, this is, as forewarned, a mere anecdote.   While I was happy to see that my sand bed had, obviously, a significant anaerobic zone, I was not happy to see so much evidence of hydrogen sulfide (and iron sulfide).  This is not ideal.  Thus, having learned of what was going on in my sand bed, I made a concerted effort to obtain more benthic organisms (worms, micro-crustaceans, seed shrimp, etc.) which would provide the necessary subtle movement in the sand to allow hydrogen sulfide to more readily exit the sand bed.  So while I'll concede that a poorly maintained sand bed with insufficient benthic life can result in significant hydrogen sulfide production, I'm not ready to concede that DSBs (even at their worst) are 'ticking time bombs' that will (or could) crash your tank and kill your animals at any time.

The Significance of Grain Size, Grain Composition and Sand Bed Dimensions

Grain Size:

Arguably, even sugar-fine is likely too large a grain size to get the full functionality of a sand bed as a source of nitrogenous waste filtration.    The reason for this is, the functionality of a sand bed as a biological filter is dependent on the existence of an anaerobic zone where anaerobic, denitrifying bacteria can carry out denitrification (in large part, the conversion of nitrogen oxides into nitrogen gas and water).   The coarser the sand, the less anaerobic space there will be.  To understand this concept, ask yourself; 'would I rather be buried under marbles or mud?'   Buried under marbles, you might stand a chance of survival since all the spaces between the marbles allow at least some air to get through.  Buried under mud, you'd suffocate in a minute or so (depending on how long you could hold your breath).   By the same general principle, a sand bed of coarse sand is going to be more oxygenated all the way through even if left undisturbed.  With a sand bed of sugar fine sand (i.e. a grain size of ~0.5mm), at the bottom of 4 inches, you'll likely get at least some anaerobic zones, but not nearly as much as with finer sand.  I'll note here that this might be the actual advantage of some 'mud' products sold as substrates for marine aquariums.  Marine mud is, after all, just very fine sand/substrate.  

All this said about the theoretical importance of grain size for creating anaerobic environments, I must tell you that some denitrification will occur even if you use marbles for substrate.   But there's even more to this issue of grain size.  The truth is that a lot of benthic (sand dwelling) organisms are very picky about the range of sediment grain size they will tolerate.   Some of them are picky to an extreme such that they will not reproduce or live a normal life span if stuck in sediment of a grain size even just 0.01mm outside of their preference.  Some organisms will just refuse to live in finer or coarser substrate.    And unfortunately, you just can't make everybody happy.  Dr. Shimek opines that a sand grain size of 0.125mm is likely a good middle ground compromise for enough benthic organisms.  Alternatively, some equally intelligent aquarists recommend using substrate of mixed grain sizes, with grains occurring across a range of 0.05mm to 0.5mm in size.  For those who wish to know more about this topic of sand grain size and the functionality of sand beds, I refer you to many articles on the subject written by Dr. Ron Shimek, Dr. Robert Toonen and others.  

In short, the thought is that finer the sand, the more effective the sand bed will be as a processor of nitrogenous waste. Keep in mind though, that, no matter how fine or coarse your sand might be, the filtration capacity of your sand bed will not appreciably increase beyond a depth of about 5 or 6 inches.  In fact, there's likely not much to be gained by having a sand bed deeper than even four inches.

 Sand Bed Dimensions:

Generally speaking, the dimensions of the 'foot print' (length x width--not depth) of a DSB should be at least ~4.5 square feet (or roughly the footprint of a 40g breeder).  Unfortunately, this recommendation is routinely given and taken without much explanation.  Generally, it's thought that this is the threshold dimension needed to maintain a healthy population of benthic organisms.  Empirically, for whatever reason, it looks like the filtration and other benefits of a DSB aren't so apparent when the dimensions are much smaller than this. Also, again, if you want to make your sand bed bigger, make it longer and/or wider (rather than deeper). 

Grain Composition:

When it comes to substrate composition, marine aquarists often find themselves choosing between aragonite and silica.  Though aragonite is usually favored, marine substrate does not necessarily have to be aragonite.  There's reason to believe, theoretically, experimentally and anecdotally, that aragonite provides *localized* alkalinity benefits which might be advantageous for any number of reasons.   For example, it might aid in phosphate precipitation and/or dinitrification.   However, any potential contribution (if any) it makes to the overall alkalinity and/or pH balance of the system as a whole is not likely significant.  Even with a sand bed of fine aragonite, you will still need to balance your system's calcium and alkalinity by some other means.  If you want to use silica sand (or 'quartz sand') and you're worried about soluble silicates, I would advise rinsing the sand *a lot.*   While quartz (SiO2) itself will not add silicates to your water (since pure quartz is virtually insoluble in water), you might be hard pressed to find 100% pure quartz sand.   Less than pure quartz sand will inevitably have some contaminates of soluble silica compounds.   However, it should be easy enough to rinse away any contaminate that's water soluble.

 Now, if I could put a side bar within a side bar, I'd discuss different commercial sources for substrate of different grain sizes and compositions.   Instead I'll just note here that there are places outside of your local aquarium store or pet store where you can find cheap substrate suitable for marine aquariums.   In addition to browsing your local aquarium store's substrate selection, don't hesitate to venture into a hardware store and/or construction supply store.   However, do be sure you know what you're getting and what you're putting in your aquarium (potential contaminates and all).

Advantages to DSBs:

If you have the time and inclination to properly set up and maintain a deep sand bed, this choice of substrate can have a lot of advantages.  Firstly, as discussed previously, it can act as an additional source of biological filtration.  Again, when set up 'correctly,' a DSB will have two zones; an upper aerobic (oxygenated) zone and a lower (oxygen depleted) anaerobic zone.  I'll note here that there are at least a few different theories and methods for setting up a DSB which focus on the deliberate construction of these layers.  The Jaubert System is one such method. 

The Jaubert System

Though arguably not a 'DSB' under my previously given definition, I'll discuss it here since it's closer to a DSB than it is to any other substrate choice.   The Jaubert system was developed by French marine biologist, Professor Jean Jaubert, in the late 1980s, and became popular in early 1990s.   In brief, this is a system with a layer of sand on top of a layer of gravel that is suspended over a thin layer of empty space.  This empty space at the bottom of the aquarium, underneath the gravel, is called the 'plenum.'  In the Jaubert system, two different types of substrate are used to create the aforementioned aerobic and anaerobic zones/layers.  Additionally, there's this 'plenum' underneath it all.  Therefore, there is water both below and above the substrate.  Supposedly and apparently, setting up the substrate in this way reduces hydrogen sulfide production and according to some aquarists, reduces nitrate levels.   Though I've never attempted to use this method myself, I (and others) have enjoyed theorizing as to what might be going on in these systems.   One such theory is that water moves through the layers by way of convection which results from a difference in temperature of the water above and below the substrate layers.  If the water on one side of the substrate layers is warmer or cooler than the plenum, convection will create a very subtle, steady 'flow' through the substrate layers.  This flow could possibly create the gas exchange needed to allow hydrogen sulfide, when/if produced, to exit the system more easily.   Or, if the gas exchange is significant enough, it might decrease the size and number of available anaerobic areas in which hydrogen sulfide production could occur.  However, this writer wonders, if the Jaubert system creates fewer anaerobic areas, how could it accomplish just as much denitrification (which also requires an anaerobic environment)?  Perhaps the reactions resulting in hydrogen sulfide production are more sensitive to the presence of oxygen than are the desired denitrification reactions.  If this is the case, then having a hypoxic environment that's not quite completely anaerobic might allow for all the same nitrate reduction while limiting hydrogen sulfide production.  However, I dare not delve too far into any detailed discussion of Jaurbert systems as this has already been done by writers far more experienced with them than myself.   There has even been some dabbling into controlled experiments aimed at comparing the Jaubert system to 'traditional' DSBs and other methods (see list of references at conclusion of this article).  Thus, I refer anyone wishing to know more about Jaubert systems to articles written by Dr. Toonen and others.

 In addition to biological filtration, DSBs create a whole other world of niches and micro-environments for marine invertebrates.  Many aquarists believe that these organisms are not only fun to watch, but also supply food (either as themselves or with their larvae) to corals and other ornamental marine animals. 


DSBs require maintenance in that, in order to function properly, they need to have sufficient populations of benthic life (both seen and unseen).  This can be accomplished in several different ways.  The best, cheapest and easiest way is to simply swipe some sand from the healthy, well-populated DSB of a fellow aquarist.  A measuring cup or two should be enough to get things going in your own sand. The next best way is to order live sand online or see if your LFS sells live sand or 'seeder sand.'  Unfortunately, just doing this once is not enough.  Over time, the diversity of your sand bed is sure to decline as some organisms out compete others into 'extinction' from your aquarium.  Thus, it's very important to occasionally repopulate your sand bed.  If not properly maintained, a DSB will become at best useless and at worst, clumps of 'cement' interspersed with black, iron sulfide coated sand.  

WARNING: Do *not* put any carnivorous echinoderms in your DSB.  These include the commonly sold 'sand sifting stars' which people mistakenly believe benefit the sand bed by stirring the sand.  To the contrary, these star fish are rapacious consumers of micro crustaceans and other benthic organisms.

The other disadvantage of DSBs is that it can be challenging to achieve a high level of water flow without creating 'sand storms.'  As previously mentioned, these sand storms can be detrimental to corals.  Also, the sand bed needs to be undisturbed by any such blunt forces (otherwise, the anaerobic zone will not form).

Shallow Sand Bed

This will be brief.  Shallow sand beds (sand beds < three inches in depth) have very few advantages.  They might add something aesthetically to a tank.  They might also add some additional niches for life.  They likely provide some marginal biological filtration and denitrification.  However, the disadvantages will almost always outweigh the minute advantages (especially in a reef tank where you'll have to contend with 'fly away' sand storms).  You can't easily vacuum a shallow sand bed during water changes.  And without the organisms of a DSB to process debris, the substrate essentially becomes a trap for fish wash, uneaten food, etc.   Thus, by and large, in my opinion, a shallow sand bed is almost always a poor choice unless it's a mere 1/4in of sand used for aesthetic purposes in a nano tank less than 15g.   While shallow sand beds have all the same disadvantages as DSBs, shallow sand beds don't have the depth necessary to harbor the life necessarily to make it a significant source of filtration or place for debris to be processed.   If you're going to go with sand and if your aquarium is 40g or larger, I say add the extra inch or two and make it a DSB.   Even if the aquarium is <40g, you might consider a remote DSB in a larger refugium rather than have a shallow sand bed in the display.

Crushed Coral     

Unlike sand, crushed coral (and similar gravel-sized substrates) can be vacuumed during water changes.  Consequently, it's relatively low maintenance.  However, this feature of crushed coral becomes less of an advantage and more of a burden the larger the aquarium size.   In large aquariums, it could take hours to vacuum all the crushed coral.  Vacuuming also disrupts any potential the substrate might have to create niches for micro marine life.  In siphoning out debris, you're going to siphon out a lot of the worms and micro crustaceans as well.  For these reasons, crushed coral is probably most advantageous when used in fish-only systems under 50g.

Remote Deep Sand Beds (Best of All Worlds?)

Remote DSBs are DSBs that are not in the display tank, but instead in an attached refugium, sump or other vessel.  Just about any water-holding container will suffice.  The nice thing about remote DSBs is that, by keeping the DSB out of the display, it's easier to have strong water flow in the main/display tank.  A remote DSB is also less likely to be disturbed by fish or yourself.    The only notable potential functional downside is that some aquarists aren't sure if a remote DSB has the same potential to provide food to corals as does a DSB in closer proximity to the animals to be fed.   Otherwise, if yourself torn between sand verses no sand, I highly recommend a well lit remote DSB/refugium.  Personally, as someone who loves marine invertebrates, I like to use the remote sand bed in a refugium as a second display.   If you add a light (as you probably should) you can grow macro algae above the sand bed for even more nutrient export.


At the conclusion of this article, I hope I've at least provided you with the questions you need to ask yourself before choosing an aquarium substrate.  As with any decision we must make in life, the most important thing to know is yourself; your abilities, desires, resources, etc.  Once you're familiar with these and all the basic information provided here, the right choice for you and your system should be easy (or at least easier) to make.

Some references and further reading:

Toonen, R.J. 1998-99. What exactly is a 'sandbed,' anyway? A brief introduction to the ecology of marine sediments, Parts 1-3. Journal of Maquaculture 6(3):42-48, 6(4):62-79, 7:2-9.

Toonen, Rob & Chris Wee (2005) Feature Article: An Experimental Comparison of Sandbed and Plenum-Based Systems: Part 2: Live Animal Experiments. Advanced Aquarists Online Magazine 

Toonen, Rob & Chris Wee (2005) Feature Article: An Experimental Comparison of Sandbed and Plenum-Based Systems. Part 1: Controlled lab dosing experiments. Advanced Aquarists Online Magazine 

Shimek, Ronald L (2003) How Sands REALLY Work, Reefkeeping Online Magazine 

Shimek, Ronald L (2001) Dearest Mudder.... The Importance of Deep Sand, Aquarium Fish Magazine

Toonen, Rob (2000) Are Plenums Obsolete? Another Viewpoint Part 2. Freshwater and Marine Aquarium (FAMA) Magazine, Vol. 23(2), pp. 44-70. 

Toonen, Rob (2000) Are Plenums Obsolete? Another Viewpoint Part 1. Freshwater and Marine Aquarium (FAMA) Magazine, Vol. 23(1), pp. 44-66.  

Sprung, Julian (2002) Jaubert's Method, the "Monaco System," Advanced Aquarists Online Magazine

And so many others'¦


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