From the bottom up: Living with your substrate

We've talked for years about tossing leaves, twigs, seed pods, etc. in our aquariums. As a community, we've elevated the art and honed the rationale for adding these materials to our aquariums. The applications for botanicals have been everything we expected they would be, and more!

What happens, though, when we allow leaves and seed pods and twigs and such to accumulate on or within the substrate in our aquariums? Over the past century or so of the aquarium hobby, it's become pretty much "doctrine" that we don't allow stuff like uneaten food, fish waste, or "detritus" to accumulate in the substrate. We're implored to regularly siphon this stuff out of our substrate and discourage its accumulation at all costs.

Now, on the surface, I totally get this. Allowing uneaten food and excessive amounts of fish waste to accumulate in your sand bed is conceivably a recipe to create a "nutrient sink" which will begin degrading the water quality of your aquairum. Sound advice, sure. I mean, no one wants to have increasing phosphate, nitrate, and other organic compounds accumulating in their tank.

I've seen many recommendations to siphon out your substrate weekly or monthly. Now, again, I don't have a problem in us preaching good habits to new aquarists: Don't overstock. Don't overfeed. Filter your aquarium properly. Complete regular water exchanges. I mean, sure, these are foundational "best practices", and part of the fundamentals of keeping fishes in a closed aquatic systems.

That being said, if you're NOT overfeeding, NOT overstocking, and conducting regular water exchanges, why is there a necessity to thoroughly siphon the substrate frequently?


Think about it for a second before you go and pelt me with stones for my heretical questioning of this "fundamental" practice in aquarium keeping. The reality is that we have been urged to siphon out "stuff" from the substrate for fear of it accumulating and degrading water quality, right? Okay, sounds good. However, consider that, in an otherwise well-managed aquarium, the organics in the substrate bacteria and other organisms which live within it.  

Ask yourself why we try to seek a balance of life forms within our aquairum. We embrace good husbandry because we want to facilitate the proper biological function within the system. And that means, "partnering" with our friends, the bacteria- to facilitate nutrient processing.

So, if you're a typical aquarist, and run a properly stocked aquarium, and embrace generally accepted husbandry practices, it seems to me that aggressively siphoning the substrate is essentially removing food resources from the bacteria and other organisms which live within the substrate. So, in our effort to keep the tank "clean", we are actually starving these organisms, and creating a sort of "dependency" on our aggressive, artificially imposed maintenance practices.

And sure, if you're disturbing an already depleted bacterial and microfaunal population within the substrate by actively siphoning it, you're creating one of those "knife's edge"situations, where the slightest possible lapse or disturbance can create potential disaster. We've talked a lot about detritus and the "bad rap" it seems to get from the hobby, to the point where you're probably sick of hearing it- but it's something I feel is very important.

Again, working with Nature and natural processes is a fundamental part of aquarium keeping. And it's a very foundational part of the botanical-style aquarium movement. I strongly believe that allowing these organisms (bacterial biofilms, fungal growths, etc.) to not only appear- but to thrive within our systems, despite their "unusual aesthetics," keeps our systems stable and healthy. Letting leaves and botanical materials break down via decomposition not only supports the overall environment within the aquarium, it fuels the lifeforms which accomplish this.

In my experience, and in the reported experiences from hundreds of aquarists who play with botanical materials breaking down in and on their aquariums' substrates, undetectable nitrate and phosphate levels are typical for this kind of system. When combined with good overall husbandry, it makes for incredibly stable systems.

I've been thinking through further refinements of the "deep botanical bed"/sand substrate relationship. I've been spending a lot of time researching natural aquatic systems and contemplating how we can translate some of this stuff into our closed system aquaria.

Now, I realize, when contemplating really deep aggregations of substrate materials in the aquarium, that we're dealing with closed systems, and the dynamics which affect them are way different than those in Nature, for the most part.

And I realize that experimenting with these unusual approaches to substrates requires not only a sense of adventure, a direction, and some discipline- but a willingness to accept and deal with an entirely different aesthetic than what we know and love. And this also includes pushing into areas and ideas which might make us uncomfortable, not just for the way they look, but for what we are told might be possible risks.

One of the things that many hobbyists ponder when we contemplate creating deep, botanical-heavy substrates, consisting of leaves, sand, and other botanical materials is the buildup of hydrogen sulfide, CO2, and other undesirable compounds within the substrate.

Well, it does make sense that if you have a large amount of decomposing material in an aquarium, that some of these compounds are going to accumulate in heavily-"active" substrates. Now, the big "bogeyman" that we all seem to zero in on in our "sum of all fears" scenarios is hydrogen sulfide, which results from bacterial breakdown of organic matter in the total absence of oxygen.

Let's think about this for just a second.

In a botanical bed with materials placed on the substrate, or loosely mixed into the top layers, will it all "pack down" enough to the point where there is a complete lack of oxygen and we develop a significant amount of this reviled compound in our tanks? I think that we're more likely to see some oxygen in this layer of materials, and I can't help but speculate- and yeah, it IS just speculation- that actual de-nitirifcation (nitrate reduction), which lowers nitrates while producing free nitrogen, might actually be able to occur in a "deep botanical" bed.

And it's certainly possible to have denitrification without dangerous hydrogen sulfide levels. As long as even very small amounts of oxygen and nitrates can penetrate into the substrate, this will not become an issue for most systems. I have yet to see a botanical-style aquarium where the material has become so "compacted" as to appear to have no circulation whatsoever within the botanical layer.

Now, sure, I'm not a scientist, and I base this on close visual inspection of numerous aquariums, and the basic chemical tests I've run on my systems under a variety of circumstances. As one who has made it a point to keep my botanical-style aquariums in operation for very extended time frames, I think this is significant. The "bad" side effects we're talking about should manifest over these longer time frames...and they just haven't.

And then there's the question of nitrate. 

Although not the terror that ammonia and nitrite are known to be, nitrate is much less so. However, as nitrate accumulates, fish will eventually suffer some health issues. Ideally, we strive to keep our nitrate levels no higher than 5-10ppm in our aquariums.  As a reef aquarist, I've always been of the "...keep it as close to zero as possible." mindset, but that is not always the most realistic or achievable target in a heavily-botanical-laden aquarium. You have a bit more "wiggle room", IMHO. Now, when you start creeping towards 50ppm, you're getting closer towards a number that should alert you. It's not a big "stretch" from 50ppm to 75ppm and higher...

And then you get towards the range where health issues could manifest themselves in your fishes. Now, many fishes will not show any symptoms of nitrate poisoning until the nitrate level reaches 100 ppm or more. However,  studies have shown that long-term exposure to concentrations of nitrate stresses fishes, making them more susceptible to disease, affecting their growth rates, and inhibiting spawning in many species. 

At those really high nitrate levels, fishes will become noticeably lethargic, and may have other health issues that are obvious upon visual inspection, such as open sores or reddish patches on their skin. And then, you'd have those "mysterious deaths" and the sudden death (essentially from shock) of newly-added fishes to the aquarium, because they're not acclimated to the higher nitrate concentrations.

Okay, that's scary stuff. However, high nitrate concentrations are not only manageable- they're something that's completely avoidable in our aquairums.

Quite honestly, even in the most heavily-botanical-laden systems I've played with, I have personally never seen a higher nitrate reading than around 5ppm. I attribute this to  common sense stuff: Good quality source water (RO/DI), careful stocking, feeding, good circulation, not disturbing the substrate, and consistent basic aquarium husbandry practices (water changes, filter maintenance, etc.).

Now, that's just me. I'm no scientist, certainly not a chemist, but I have a basic understanding of maintaining a healthy nitrogen cycle in the aquarium. And I am habitual-perhaps even obsessive- about consistent maintenance. Water exchanges are not a "when I get around to it" thing in my aquarium management "playbook"- they're "baked in" to my practice.

So yeah, although nitrate is a concern in botanical-style aquariums, it need not be an ominous cloud hanging over our success.

Relatively shallow sand or substrate beds seem to be optimal for denitrification, and many of us employ them for the aesthetics as well. Light "stirring" of the top layers, if you're concerned about any potential "dead spots" is something that is permissible, IMHO. Any debris stirred up can easily be removed mechanically by filtration, as mentioned above. Of course, as we already discussed, you don't have to go crazy siphoning the hell out of your sand every week, essentially decimating populations of beneficial microscopic infauna -or interfering with their function- in the process.

Okay, so I think we have at least started to beat the shit out of the biological aspects of substrate composition and maintenance...Let's circle back to aesthetics for a second.

I think one of the most "liberating" things we've seen in the botanical-style aquarium niche is our practice of utilizing the substrate itself to become a feature aesthetic point in our aquariums, as well as a functional mechanism for the inhabitants.

In other words, in a strictly aesthetic sense, the bottom itself becomes a big part of the aesthetic focus of the aquarium, with the botanicals placed upon the substrate- or, in some cases, becoming the substrate! These materials form an attractive, texturally varied "micro-scape" of their own, creating color, interest, and functions that we are just starting to appreciate. In fact, I dare say that one of the next "frontiers" in our niche would be an aquarium which is just substrate materials, without any "vertical relief" provide by wood or rocks.

I've executed a few aquariums based on this idea (specifically, with leaves), and I've been extremely happy with their long-term performance! Oh, and they kind of looked cool, too...

Nature provides no shortage of habitats with unusual substrate composition for inspiration. If we look at them in context of the surrounding terrestrial ecosystem, there are a lot of possible "functional takeaways" that we as hobbyists can apply to our aquarium work.

And the interesting thing about these features, from an aesthetic standpoint, is that they create an incredibly alluring look with a minimum of "design" required on the hobbyists' part. Remember, you can to put together a substrate with a perfect aesthetic mix of colors and textures, but that's about it.

We have to "cede" some of the "work" to Nature at that point!

Once your substrate is in place, Nature takes over and the materials develop that lovely "patina" of biofilms and microbial growth, and start breaking down. Some may be moved about by the grazing activities of resident fishes, or otherwise slowly redistributed around the aquarium. I suppose the degree to which this happens is dependent upon the type of substrate material you utilize.

And of course, we're finding that it's not just us who are interested in unique substrate materials...You guys are snapping up our NatureBase sedimented substrates at a rate that even we couldn't have expected. You "get" the idea behind it. But, let's review it one more time, really quickly.

So, yeah, you'll have to make a mental shift to appreciate a different look and function with our sedimented substrates. And many hobbyists simply can't handle that. We've been up front with this stuff, to ward off the, "I added NatureBase to my tank and it looks like a cloudy mess! This stuff is SHIT!" type of emails that inevitably come when people don't read up first before they purchase the stuff.

The igapo and varzea substrates were intended to be "terrestrial" for a period of time, to get the grasses and plants going, and then inundated.  You DON'T RINSE THEM BEFORE USE! You CAN fill them with water right off the bat; however, you should be ready for some cloudy water for a week or more! That's just because of their unique composition.


This is not unlike what occurs in the wild habitats...newly inundated forest floors have a lot of leaf litter, seed pods, etc., and will be quite turbid for some time. If you understand the context for which they are intended, and the habitats which they help to replicate, this is perfectly acceptable and logical...Of course, you need to make that "mental shift", right?

And yeah- you CAN use them in a more "conventional" manner right from the start- if you understand the way they will impact the look of your tank for a while.

Although these substrates can grow both terrestrial and aquatic plants well, they were not intended to be "generic planted tank substrate", specifically. We're not trying to compete with the many fantastic specialized planted aquarium substrates out there. This is not some "Tannin is coming for you!" B.S. Rather, these substrates are modeled after relatively nutrient-poor soils, which will grow plants well, but likely not as well as the fancy clay pellets and such that are formulated specifically to grow aquatic plants.


Yeah, our Igapo and Varzea mixes can grow plants like grasses and marginals pretty well. And, we ARE hearing about pretty good aquatic plant growth from users, too. However, I'd imagine that you're likely not going to be doing your next "Dutch-style" aquascape or "Iwagumi" with our NatureBase substrates. And, because of their price, you simply aren't likely to do a 50 or 100 gallon tank with them!

mean, you could, but...

Our Igapo and Varzea substrates mimic sandy acidic soils that have a low nutrient content. And, as you know, the color and acidity of the floodwater is due to the acidic organic humic substances (tannins) that dissolve into it. The acidity from the water translates into acidic soils, which makes sense, right?

Much like in Nature, the materials that we place on the bottom of the aquarium will become an active, integral part of the ecosystem. From a "functional" standpoint, bottoms comprised of our substrates supplemented with a variety of botanical materials form a sort of "in-tank refugium", which allows small aquatic crustaceans, fungi, and other microorganisms to multiply and provide supplemental food for the aquarium, as we've touched on before.

They've become not only physical places for fishes to hide and forage among- they've become an integral part of the entire closed aquarium ecosystem itself, helping influence water parameters, foster growth of fungi and microorganisms, and just maybe- some form of nutrient export/denitrification (although that last part is still a bit speculative).

It's certainly no stretch to call our use of botanicals as a form of "active substrate", much like the use of clays, mineral additives, soils, etc. in planted aquariums. Of course, we're not talking about plants in this context...

Although our emphasis is on creating specific water conditions, fostering the growth of microorganisms and fungi, as well as creating unique aesthetics, versus the "more traditional" substrate materials fostering conditions specifically for plant growth.

And, as we play more with botanicals, we're finding out more unique ways to work with interesting materials to create substrate-centric systems that check all the boxes: Functionality. Interest. Aesthetics. Stability.


We've talked about "functional aesthetics" created by botanicals in the aquarium, the potential for additional biological support/filtration (and potentially even denitrification), and it's a big, BIG topic, with lots more to be explored, discovered and deployed in our aquarium...flirting with a "substrate-only"- or "substrate-focused" tank is one of those tantalizing, at first seemingly awkward, yet ultimately transformational little projects we can play with! 

Let's keep on this stuff. Let's keep questioning aquarium hobby dogma, but let's not become dogmatic. If we're off on our assertions, let's figure out why, and see just what is actually happening. It's all one big, grand experiment- and everyone is invited to play!

Stay excited. Stay motivated. Stay curious. Stay unique. Stay observant. Stay creative...

And Stay Wet.


Scott Fellman

Tannin Aquatics  




Scott Fellman
Scott Fellman


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