Freshwater Deep Sand Beds Work

by Deirdre Kylie


What is a deep sand bed?

A deep sand bed is a sand substrate coupled with bacteria and multicellular organisms working together as a powerful biological filter. Originally developed in the saltwater aquarium hobby, deep sand beds (DSBs) extended the biological filter from converting ammonia and ammonium to nitrate, to eliminating nitrate by denitrification - using the oxygen in nitrate, releasing harmless nitrogen or nitrous oxide. This was desirable because of saltwater organisms’ great sensitivity to nitrate. In freshwater, nitrates are much less toxic, requiring infrequent water changes to control levels, but the freshwater DSB as described in this article does more than eliminate nitrate.


How does the Freshwater DSB work? What does it do?

Primarily, freshwater DSBs are biological filters, eliminating ammonia, nitrite, nitrate, hydrogen sulfide, byproducts of decay, and solid waste (mulm). Secondarily they are good planting mediums because decaying organic matter disintegrates and sifts into the sand, releasing carbon dioxide and minerals which boost plant health and growth.



How deep sand beds work. © Deirdre Kylie




Biofiltration is accomplished by bacteria working in concert with multicellular organisms. Sand provides enormous surface area for bacterial growth. Grains approximately 0.25 mm (0.01 inches) across with roughly cubic shapes have a surface area of about 1.5 square mm (0.12 square inches). In a 30 x 30 cm (12 x 12 inch) patch of sand 1 cm (0.4 inches) deep, there will be 57.6 million grains with a total surface area of 86.4 square meters (1314 square feet) which is about 0.13 square meters (1.4 square feet) of surface area within a cubic centimeter (0.06 cubic inches) of that grain size sand.


Multicellular organisms enhance the size and function of, or the nutrient flow through and between bacterial colonies by improving diffusion within the sand bed. Burrowers dig into the sand, loosening it up, sometimes from the water/sand interface down to the anaerobic zone as is the case with the California Blackworm, Lumbriculus variegatus, an aquatic cousin of the common earthworm, which lives similarly but submerged and in muck. Plants can extend their roots into anoxic zones where their oxygen allows aerobic hydrogen sulfide eating bacteria access to the source while the roots get access to soluble mineral nutrients released by anaerobic bacteria. Scavengers such as snails and planarians breakdown mulm, helping it sift into the sand where it feeds the different bacterial communities.


Principles by which effective Freshwater DSBs operate


Ready infiltration of mulm and diffusion of soluble substances throughout the sand bed: The looser and more resistant to compaction the sand the further and faster infiltration and diffusion reaches.  Multicellular organisms enhance diffusion and infiltration, which permit organisms from different environments throughout the sand bed to interact as a system.


Aerobic, anaerobic, and anoxic environments must not be disrupted too much: Bacteria in the freshwater DSB, must have stable environments. Disturbances in the sand disrupt diffusion of materials from one environment to the other. This principle prohibits any thing or activity which mixes sand together from the aerobic, anaerobic, and anoxic layers. Undisturbed sand permits each population to do its job and for diffusion to link environmentally segregated organisms.


Microbes and multicellular organisms of the Freshwater DSB make up a mini-ecosystem: Each organism effects the others -- they are an interconnected community. This principle allows the freshwater DSB greater biofiltration capacity; few organisms can act singly. This ecosystem is only possible if supported by the prior two principles.



Small freshwater worms like Lumbriculus spp. move into the anaerobic areas of the sand to some degree, but will not substantially disturb the separate layers of the deep sand bed. © Deirdre Kylie




Essential Practices in keeping Freshwater DSBs:
These practices support the principles of effective freshwater DSB operation.


NOT disturbing the sand: Stirring and vacuuming to disrupt anaerobic pockets makes sand beds less productive by disrupting the activity of bacterial populations. If oxygen is introduced to anaerobic and anoxic zones, denitrification and iron and manganese reduction comes to a stop. Disrupting the sand also interrupts the diffusion which connects one environment to another.

If you MUST vacuum, hold the vacuum above the sand so that only what is resting on it is sucked up -- leave that sand alone!


If you MUST unearth a root system, jiggle it rapidly but without much force as you slowly pull it from the sand. This leaves the sand close to its original place in the bed.


WHEN you plant plants, use a tool which allows you to grip their roots and insert them with as little disruption to the sand bed as possible. Make an exception if the root system is massive or the plant delicate.


Allowing mulm to accumulate: Use relatively weak (max flow 50% of tank volume/hour) filtration and no vacuuming (unless there’s an ungodly amount of mulm). Mulm is a healthy constituent of freshwater DSBs. It is harmless and in fact supplies the freshwater DSB minerals and organic matter.


Leaving root systems in the sand: Decaying roots release carbon dioxide and nutrients into the sand. When moving a living plant which can will tolerate it or removing dead or dying plants, cut them from their root systems. Leave the roots in place. This avoids disturbing the sand. Plant amongst the dead roots. If the sand has buried, decaying roots everywhere, you can remove further ones at your discretion; too much decay overwhelms the biological filter’s capacity to process ammonia. Fewer decaying roots merely means less carbon dioxide and nutrients and slower plant growth.


Constituents of the freshwater deep sand bed

Good Sand: Essential for a healthy sand bed. The nature of the sand greatly effects how the sand bed performs. Good sand resists compaction and is chemically neutral. Pool filter sand fits that bill as do many river sands. So will many quartz based sands. Sand meshed for a consistent, small range of grain sizes, such as pool filter sand is, is compaction resistant. A grain size of approximately 0.21 mm (70 mesh) to 0.54 mm (35 mesh) is the sweet spot for aquarium use. Sand meshed for a limited range of grain sizes compacts less than sand with a wide range of grain sizes. "Good" sand is good for a few reasons: quartz sand doesn’t affect water chemistry and loose sand supports the ready infiltration of mulm and diffusion of soluble nutrients, gases, and other substances throughout the sand bed.


Bacteria: In an established freshwater DSB there are too many species to go into or name in this article but suffice it to say that they perform nearly all of the functions of the DSB. Bacteria live in communities segregated by oxygen tolerance. Interconnected by diffusion through the sand, they work as a system: nitrifying bacteria metabolize ammonia into nitrate and denitrifying bacteria reduce the nitrate to nitrogen gas; some nitrate reducers use nitrate to oxidize hydrogen sulfide; other bacteria break down organic compounds via fermentation while others reduce iron and other metals which rooted plants absorb; yet others aerobically decay the mulm, liberating ammonia; finally, all bacterial communities produce carbon dioxide.


Multicellular organisms: Rooted plants, Californian Blackworms, planarians, and Malayan Trumpet Snails (Melanoides tuberculata) enrich and/or enlarge the environments within the freshwater DSB, thus enhancing its function.




Tubifex worms may be used in a freshwater deep sand bed. © Deirdre Kylie




Note that it is not essential in implementing a freshwater DSB that the species used actually be those named here, but rather that whatever organisms you do use perform the same general function. Each supports at least one key principle of functional freshwater DSBs. For example, Tubifex worms (Tubifex Tubifex) will do the same job as California Blackworms, so may be used instead. Similarly, the Assassin Snail (Clea helena) snails burrow through the sand just like Malayan Trumpet Snails, and may be used alongside them as biological control, since they catch and eat Malayan Trumpet Snails.


Editorial note: Tubifex worms can be a source of infections, including Whirling Disease, Myxobolus cerebralis, so a reliable source of worms, for example from a fish-free garden pond, is recommended.


Rooted Plants: Plants store carbon, soak up heavy metals, and the roots carry oxygen into anaerobic and anoxic regions where it supports aerobic bacteria as they absorb mineral nutrients there.


Aerobic bacteria living amongst the roots oxidize hydrogen sulfide and other metabolic byproducts of anoxic and anaerobic bacteria. This way, plants contribute to the safety of deep sand beds.

Roots accumulate carbon and minerals as living tissue as they grow. They release carbon dioxide, minerals, and other nutrients when they die and decay.


Finally, plants absorb heavy metals and other toxins from both substrate and water column.


California Blackworms: These burrow from the sand/water interface into the anaerobic layer, enhancing diffusion, especially of oxygen, to the anaerobic levels and back. This pushes down the anaerobic layer and expands the aerobic layer.


The worms eat decaying organic matter and bacteria in mulm, waste which can sift deeper into the sand.


Finally worms are a great live food! The fish and certain shrimp go after them so enthusiastically that one often must periodically re-stock the worms.


Planarians: Also known as flatworms, these unsegmented, dorso-ventrally flatted worms such as Dugesia tigrina. They are small, usually 21 mm (0.83 inches) or less. Although related to the parasitic flatworms called flukes, these free-living flatworms are harmless. They eat organic matter and bacteria, crawling through the sand to find it. They digest the matter into fine particles, which infiltrate the sand bed faster and which bacteria break down quickly.


Malayan Trumpet Snails: These livebearing snails help break down mulm and slowly turn over the aerobic layer, extending its depth without overly disrupting its bacteria. Churning the sand works mulm in and improves the exchange of oxygen and other gasses/chemicals up and down through the top layer.


Malayan Trumpet Snails are seen by some as the solution to the “problem” of anaerobic sand. However they do not burrow more than 1 inch/2.54 cm down. There’s no oxygen below that depth, so the snails can’t dig any further down.


Malayan Trumpet Snails are useful, easy to obtain additions to the deep sand bed community. © Neale Monks





Mulm: Mulm, the accumulated crud of decaying matter in the tank, is essential to the freshwater DSB. It is a source of energy and nutrients for the bacteria of the freshwater DSB. It provides food of the burrowing snails, planarians and blackworms, as well as minerals for root feeding plants.


Without mulm in your DSB you would have a basic nitrifying biofilter which would depend on the nutrients found in aquarium water. Plant growth would be at best hum-drum without supplemental fertilizers.


Setting Up a Freshwater DSB aquarium:
Choose a tank and consider whether to go high-tech or keep it simple. The freshwater DSB is well suited to low-tech and high-tech setups. It’s your choice so long as there will be sufficient nutrients, light, and carbon dioxide for the plants.


1. Fill the aquarium with approximately 3 inches of good sand - pool filter sand, specialized horse racetrack sand, and other meshed sands are good choices.

2. Add water and whatever chemical additives you choose. A PH of 6.8 is good for most aquatic plant. Buffers are not a terrible idea but phosphate based buffers can kill certain phosphate sensitive plants, shrimp, and scuds even at moderate levels.

3. Put an internal filter or power head rated for at very most half the size of the tank; it will be perfectly adequate in this case and allow mulm to settle. No biomedia is needed though there’s nothing wrong with using it; mechanical filtration is adequate. Do not use aeration or a filter which splashes; it blows off any surplus carbon dioxide. Instead, position the outlet of the filter/powerhead to disrupt the surface layer/surface tension. Smooth roils sufficiently boost oxygenation to support a surprising number of fish for your tank without driving off carbon dioxide.

4. Add a heater if this is to be a warm water tank. Cold water DSBs work but with less capacity as a biofilter. Keep it at 80º to 82º when cycling the tank to speed the process.

5. If you can, get a sample of sand from an established freshwater DSB or planted tank with a sand bed. Spread it across and stir it into the sand bed. This introduces a diverse bacteria to the budding biofilter.

6. Cycle the tank however you like. A fishless cycle using fish food to generate the ammonia is a good way to go: Put small pinches of flake into the tank daily until the goal level of ammonia/ammonium is close, then cycle the tank as usual. Decaying food remaining in the tank will continue to produce ammonia for days. If ammonia levels continue to rise excessively, you should vacuum the remaining food on the bottom to cause it to level off.

7. Place decor and plants. You can start with a modest number and propagate them while your sand bed matures or you can just dose with fertilizer, plant heavily, and bypass months of development. Slow development by stages lets one get to know the freshwater DSB and aquascape with more depth and detail than snap designing and planting can achieve. However you do it, include plants which develop deep, extensive root systems.

8. Add a tablespoon of California Blackworms per ten gallons, a handful of Malayan Trumpet Snails, and a few planarians (which you can often find in another aquarium. You may also add any other creatures that might contribute to the function of the DSB. Let the inverts settle in overnight, without any fish in the tank. Many fish will view these animals as live food, so giving them some time to settle in and burrow into the sand is crucial.

9. Finish stocking. With the sand bed’s massive biofilter and the filter’s outflow gently stirring the surface, you can stock to any reasonable level so long as you introduce stock a few at a time as with any other aquarium. Beware of too little oxygen, excess carbon dioxide, and possibly ammonia. Additionally, too much nitrate will overwhelm the biofilter’s capacity for denitrification well before ammonia overwhelms the capacity for nitrification.


Deep Sand Beds are Safe:

The essential principles and practices of this article will yield a freshwater DSB that is not a threat to livestock and doesn’t stink. In San Francisco, keeping an 8 cm (3 inch) deep sand bed in one’s tank is common practice and there’s a favorite LFS where every tank has a freshwater DSB and is stocked with very healthy fish. Locally to SF, anecdotes of toxic disasters and stinks due to sand beds are nonexistent.


Improperly implemented and kept, a freshwater sand bed -- deep or not -- will be the sort which stinks of rotten eggs, which you have to hand-stir or deep vacuum for fear of dreaded anaerobic decay which is the subject of all those stories about the fishkeeper disrupting an anaerobic pocket thus releasing a bubble of hydrogen sulfide and killing all the livestock very quickly.


While some tales of anaerobic disasters surely are true, bubbles from the substrate rise too quickly and have too little surface area to sufficiently contaminate a even a small tank. It’s more likely that dissolved gases and toxins from anaerobic decay were released into the water column when they were disrupted by the fishkeeper. Bubbles percolating up through the sand leave it to harmlessly close up behind them without even mixing much - this phenomenon can easily be observed in bubbles which form against the glass because the anaerobic sand is black and contrasts with the oxygenated sand.


Important Acknowledgement

Though my tanks are not Walstad tanks, they are inspired and informed by Diana Walstad’s method and information as presented in her wonderful book, "Ecology of the Planted Aquarium." I suggest that book as a great source of information about nutrients, bacteria, lighting, etc., comprehensible to the layperson. Without it, I might have red and blue epoxy covered gravel, plastic plants, some overcrowded goldfish, and little enthusiasm for the hobby.

FW Substrates on WWM :


     Freshwater Substrates by Bob Fenner,  Nice bottoms; Choosing the right substrate for your aquarium by Neale Monks, Freshwater Deep Sand Beds Work by Deirdre Kylie, & Related FAQs: Freshwater Substrates 1, FW Substrates 2, Freshwater Filtration, Freshwater Set-up
FAQs on: FW Substrate Selection, FW Substrate Physical Properties, FW Substrate Chemical Properties, FW Substrate Amounts & Placement, FW Substrate Changing, Moving, Adding To, FW Substrate Cleaning, FW Substrate Issues, FW DSBs,

WWM Sponsor /Adverts


Quality Marine

CPR Aquatic



That Fish Place / That Pet Place

Marine and Reef

Champion Lighting


Bulk Reef Supply

Premium Aquatics

Aqua Cave