Bottom-up evolution...

Don't you just love the idea of "tweaking" your aquariums from time to time? You know, working with new ideas that might create some different outcomes in existing tanks...or even just starting new tanks with completely different ideas and running with them.

I guess it's sort of my "process", right?

Like many of you, I'm constantly "iterating", or in our language, "evolving" my aquariums to embrace new ideas, concepts, or aesthetics which I think would push the "state of the art" of blackwater/botanical-style aquariums down the road a bit.

Lately, I've been thinking about an even more realistic-looking-and functioning- "flooded forest" themed aquarium, something we're seeing more and more of our community playing with. And, part of my experimentation has been playing with different substrate compositions, depths, and particle sizes.

And, while playing with those ideas, I've been thinking through further refinements of the "deep botanical bed"/sand substrate relationship. I've been spending a lot of time researching the natural 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 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 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 operations 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, 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. In my opinion, the far more problematic issues with botanicals and water quality are related to lapses in our own good judgment and to misguided practices. Experience with our customer base tends to confirm this, too.

The very few issues that we've seen with people "pushing it too far" in terms of botanical applications, were caused by rapid influxes of large quantities of botanical materials to existing, stable aquariums, which, I believe, overwhelmed the resident bacterial population and might have resulted in rapid oxygen depletion and a corresponding increase in CO2. The result was fishes hanging at the surface in an attempt to get oxygen. The good news was that almost every situation like this I heard of was remedied in a relatively short period of time by adding additional aeration into the tank, a series of water exchanges, and/or removing some of the materials.

Generally, loss of life was minimal (that's an awful term, though) or nonexistent as a result of these measures. Regardless, it's really important to be careful. Fish can die if we push it too hard.  It's not just "Boil, dump...Instant Amazon..."  Measured implementation and experimentation is required when using botanicals. We're often adding biological materials to established aquariums, which might not be able to handle large, fast influxes.

There's obviously some "upper limit" of how much botanical material we can add to a given established  system in a brief period of time, and it's especially more profound in newly-established aquariums with "immature" nutrient export mechanisms in place.

Typically, most botanical-"powered" systems run trouble free, especially when you understand what's going on, know what to expect (yeah, decomposing leaves, biofilms, etc.), and have mechanisms in place to accommodate them.

Now, this is not to say that you can't have some disasters if you "go too hard" or "too fast" with lots of botanicals in a closed system. It just makes sense, right? You're adding material which will decompose in the water, and if adequate nutrient export systems are not in place to deal with it, you could have some problems. This isn't some new revelation; it's something we've been talking about here for a long time.

And it's common sense- "Aquarium-Keeping 101", really. However, it's important to bring up the potential "dark sides" of botanical-style aquariums now and again, as more and more hobbyists start experimenting with this stuff.

What kinds of things can we do to prevent problems like this?

Well, for one thing, we can add botanical materials gradually, at a slow, steady pace. This will give our bacteria population a chance to catch up with the influx of materials being added. Also, it will slow down the pace of any pH fluctuations (assuming we are utilizing stuff that can lower the pH in our tanks) so that the fishes can adjust to them.

It's common sense "best practice" for us.

Another thing would be to employ good circulation within your system, which not only results in greater oxygenation and "mixing" of water "strata" - it physically suspends fine particulates in your system as well, making it easier for mechanical filtration to remove (of course, that assumes you don't like the look of "stuff" in the water, as some of us do!).

So, back to the substrate again...

Relatively shallow sand beds seem to be optimal for denitrification, and many of us employ them for the aesthetics as well. Light "vacuuming" of the top layers to remove any potential "dead spots" is always a good practice, IMHO. Any debris stirred up can easily be removed mechanically by filtration, as mentioned above. Of course, 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.

Now, I think one of the most "liberating" things we've seen in the blackwater, 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.

A literal "active substrate", indeed! Yet, something that is fascinating and beautiful for those who give the idea a shot!

This is a big aesthetic shift in the hobby, but it goes well beyond that.

I mean, sure, we've done hardscapes before, with wood and stones dominating the 'scape.  Aesthetics are great. They create alluring aquariums. However, our tanks have placed far more emphasis on the "functional" aspects of the botanical materials we use. The aesthetics just sort of go with the territory. 

Ahh, the "function" part of the equation...

Much like in the wild aquatic habitats of the world, the materials that we place on the bottom of the aquarium will become an active, integral part of the ecosystem. From a "functional" standpoint, substrates comprised of various grades of sands, muds, and silts, 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.

Just like in Nature.

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 nutrient-processing 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. 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.

Of course, there is nothing saying that you can't incorporate the best of both worlds, to create aquariums which offer our fishes AND our plants optimum environmental conditions in which to grow and multiply.

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 just scratched the surface about the "functional aesthetics" created by botanicals in the aquarium, and 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 aquariums!

Flirting with a "substrate-centric" tank is one of those tantalizing, at first seemingly awkward, yet ultimately transformational little projects we can play with. 

And then there is the use of aquatic plants; something that we are seeing more and more of in botanical-oriented systems. In fact, it's becoming a real "standard" in our world- as it should be- as it realistically represents many of the wild habitats from which our fishes hail.

In terms of impact on the substrate, it's a known fact that plants remove ammonia directly, and typically will prevent the anaerobic conditions that promote production of hydrogen sulfide within the substrate itself. So there are many benefits to including them in our botanical-style blackwater aquariums!

 In summary, the simple practice of adding "botanical stuff" into our aquariums is not some "high concept thing." However, the impacts on the water chemistry and overall aquatic environment- not to mention, on our fishes- are profound, fascinating, and real!

Being careful and taking the time to clean, prepare, and add botanicals to your aquarium in a measured manner always yields a better outcome. Going slowly also gives you the opportunity to address any issues that you might have before they become critical, especially when you're experimenting with some of these ideas.

It just makes sense to be patient. The rewards are so great.

We as an enthusiastic and engaged global community have slowly and carefully taken the concept of a blackwater, botanical-style aquarium out of the realm of "carnival side show" into an evolving, legitimate practice to achieve significant results with our treasured fishes. We continuously see reports of dramatic fish health improvements, spawnings of delicate species, seen wonderful, realistic representations of nature, even experienced an occasional tragedy or two on very rare occasions...and realized from each- that we learn.

And we recognize that we are all part of a greater whole, and that the work that we're doing will benefit the generations of aquarists who will follow us, and apply what we're learning in ways that we probably haven't even contemplated yet. Thinking about things like botanical-infused substrates are just one way to push the state of the art along.

Yeah, it's a hobby evolution...from the bottom up.

Glad to have you in the mix!

Stay creative. Stay enthusiastic. Stay bold. Stay curious. Stay engaged...

And Stay Wet.


Scott Fellman

Tannin Aquatics 



Scott Fellman
Scott Fellman


Leave a comment