I've embarked on some "remodels" of some of the aquariums in my home office, and it's been a most interesting experience- as it always is. I've taken a slightly different approach to these "makeovers" over time. Specifically, one of the things I've done in recent years is to keep the substrate layers from the existing tanks and "build on them." 


In other words, I'm taking advantage of the well-established substrate layers, complete with their sediments, decomposing leaves and bits of botanicals, and simply building upon them with some additional substrate and leaves. I've done this many times over the years- it's hardly a "game-changing" practice, but it's something not everyone recommends or does.

I believe that preserving and building upon an existing substrate layer provides not only some biological stability (ie; the nitrogen cycle), but it has the added benefit of maintaining some of the ecological diversity and richness created by the beneficial fuana and the materials present within the substrate.  I know many 'hobby old timers" might question the safety- or the merits-of this practice, mentioning things like "disturbing" the bacterial activity" or "releasing toxic gasses", etc. I simply have never experienced any issues of this nature from this practice. Well maintained systems generally are robust and capable of evolving from such disturbances. 

I see way more benefits to this practice than I do any potential issues.

Since I tend to manage the water quality of my aquariums well, I have never had any issues, such as ammonia or nitrite spikes, by doing this- in fresh or saltwater systems. It's a way of maintaining stability- even in an arguably disruptive and destabilizing time!

This idea of "perpetual substrate"- keeping the same substrate layer "going" in successive aquarium iterations- is just one of those things we can do to replicate Nature in an additional way. Huh? Well, think about it for just a second...

In Nature, the substrate layer in rivers, streams, and yeah, flooded forests and pools tends to not completely wash away during wet/dry or seasonal cycles.

Oh sure, some of the material comprising the substrate layer may get carried away by currents or other weather dynamics, but for the most part, a good percentage of the material- and the life forms within it- remains.

So, by preserving the substrate and "refreshing" it a bit with some new materials (ie; sand, sediment, gravel, leaves, and botanicals), you're essentially mimicking some aspects of the way Nature functions in these wild habitats. And, from an aquarium management perspective, consider the substrate layer a living organism (or "collective" of living organisms, as it were), and you're sure to look at things a bit differently next time you re-do a tank!

It's hardly "radical" in it's departure- you've likely done a version of this hundreds of times during your aquarium hobby career: It's the idea of keeping your aquarium more-or-less "intact" while moving on to a new iteration.

In other words, let's say that you're kind of over your Southeast Asian Cryptocoryne biotope, and ready to head to South America. So, rather than tearing up the entire tank, removing all of the plants, the hardscape, the leaves and botanicals, and the substrate, you opt to remove say, only the plants, some botanicals, and the hardscape materials from the tank; exchange a good quantity of the water.

Woooah! Crazy! You fucking rebel...

I know. I know. This isn't exactly earth-shattering. 

On the other hand, it IS a bit of a departure, at least on a philosophical level, from the idea of just "starting over from scratch" that is the more common approach in our hobby.

And, in the world of the botanical-method aquarium, the idea of leaving the substrate and leaf litter/botanical "bed" intact as you "remodel" isn't exactly a crazy one. And conceptually, it's sort of replicates what occurs in Nature, doesn't it?

Yeah, think about this for just a second.

As we almost constantly discuss, habitats like flooded forests, meadows, vernal pools, igarape, and swollen streams tend to encompass terrestrial habitats, or go through phases where they are terrestrial habitats for a good part of the year.

In these wild habitats, the leaves, branches, soils, and other botanical materials remain in place, or are added to by dynamic, seasonal processes. For the most part, the soil, branches, and a fair amount of the more "durable" seed pods and such remain present during both phases.

The formerly terrestrial physical environment is now transformed into an earthy, twisted, incredibly rich aquatic habitat, which fishes have evolved over eons to live in and utilize for food, protection, and complex, protected spawning areas. 

All of the botanical material-shrubs, grasses, fallen leaves, branches, seed pods, and such, is suddenly submerged; often, currents re-distribute the leaves and seed pods and branches into little pockets and "stands", affecting the (now underwater) "topography" of the landscape.

Leaves begin to accumulate. Detritus settles...

Soils dissolve their chemical constituents- tannins, and humic acids- into the water, enriching it. Fungi and micororganisms begin to feed on and break down the materials. Biofilms form, crustaceans multiply rapidly.  Fishes are able to find new food sources; new hiding areas to spawn.


It's a concept that we should think about more when managing and evolving our tanks: The idea that Nature doesn't just "break down" a habitat and start from scratch. Rather, it simply evolves and reacts to changes in the environment.

That should be our model. That should be our process. 

You can change up an aquarium without tearing it completely apart and starting entirely from scratch. You can leave substrate intact, and keep a fair amount of the botanical material that's already in the tank "in play."

IMHO, like 90% of the battle in establishing successful botanical method aquariums (or any type of system, really) is to introduce and manage a biome of life forms which will help the tank flourish over the long term.

If you approach things with the mindset that detritus is food for someone, you won't feel the sense of urgency to siphon it all out when re-working your tank. Rather, you'll understand that keeping it in the aquarium substrate is beneficial; it literally helps "power" the ecology of the aquarium. They key, of course, is not to have it sitting in there in excess.

Keeping the ecological "engine" which powers your tank alive during these transitions is the key to a "continuous" aquarium- one which can endure multiple "thematic" changes over it's (possibly indefinite) service lifetime.

It's all about ecology. Bringing up a biome. Creating a living system within the confines of an aquarium. Understanding that some of the things that we've taken for granted, or even things that we've been afraid of, are among the most important  things that we can do for our tanks.

The idea of keeping a tank going indefinitely in many permutations is nothing new or novel in the aquarium hobby, really. However, thinking about it holistically, and executing a plan to keep it going is a different thing altogether.

Perhaps it is most important to look at biology over almost any other aspect of aquarium keeping. In other words, to accept that the biological interactions and the establishment of a biome within the aquarium are the keys to pretty much everything that we do.

Keeping a tank over the long term is not all that challenging, once we accept the fact that creating and maintaining the biome of the system is of utmost importance, the actual processes and techniques are really secondary. And botanical materials in the aquarium helps create a long term habitat for the biome- a collection. of microorganisms and other life forms- to thrive and multiply.

Yeas, one of the underlying "core principles" of the botanical method aquarium is that having a bunch of leaves and other botanical materials present in the aquarium fosters a larger, more diverse population of these valuable organisms, capable of offering supplemental food sources to fishes and processing organics, thus creating a more stable, robust ecology in the aquarium.

With a matrix of materials present, the bacteria (and their biofilms- as we've discussed a number of times here) have not only a "substrate" upon which to attach and colonize, but an "on board" food source which they can utilize as needed.

Facultative bacteria, adaptable organisms which can use either dissolved oxygen or oxygen obtained from food materials such as sulfate or nitrate ions, would also be capable of switching to fermentation or anaerobic respiration if oxygen is absent.


Well, that's likely another topic for another time. Something we've hinted at in the past, but haven't really analyzed much in the aquarium context. We'll revisit it. For now, let's focus on some of the other more "practical" aspects of this "biome" thing. production for our fishes.

In the case of our fave aquatic habitats, like streams, ponds, and inundated forests, epiphytes, like biofilms and fungal mats are abundant, and many fishes will spend large amounts of time foraging the "biocover" on tree trunks, branches, leaves, and other botanical materials.

The biocover consists of stuff like algae, biofilms, and fungi. It provides sustenance for a large number of fishes all types.

And of course, what happens in Nature also happens the aquarium- if we allow it to, right? And it can function in much the same way?


I have long felt that a botanical-method aquarium, complete with its decomposing leaves and seed pods, can serve as a sort of "buffet" for many fishes- even those who's primary food sources are known to be things like insects and worms and such. Detritus and the microorganisms within it can provide an excellent supplemental food source for our fishes!

Sustenence...from the microbiome.

It's well known that in many habitats, like inundated forests, etc., fishes will adjust their feeding strategies to utilize the available food sources at different times of the year, such as the "dry season", etc.

And it's also known that many fish fry feed actively on bacteria and fungi in these habitats...So I suggest once again that a botanical-style aquarium could be an excellent sort of "nursery" for many fish and shrimp species! 

Again, it's that idea about the "functional aesthetics" of the, botanical-style aquariums. The idea which acknowledges the fact that the botanicals we use not only look cool, but they provide an important function (supplemental food production) as well. As we repeat constantly, the "look" is a collateral benefit of thef unction.

This is a profoundly important idea.

Perhaps arcane to some- but certainly not insignificant.

And who we do a tank "makeover", I feel that there is little sense in siphoning out the detritus and decomposed botanical materials which may have accumulated in the tank. Because this stuff will continue to provide an ecological "foundation" for your "makeover" aquarium. Just "build" upon it, like Nature does.

Nature doesn't waste anything- and neither should we. 

And of course, we've talked before about the "botanical nursery" concept- creating an aquarium for fish fry that has a large quantity of decomposing botanicals and leaves to foster the production of these materials, which serve as supplemental food for your fish fry.

I have done this before myself and can attest to its viability. You fishes will have a constant supply of "natural" foods to supplement what you are feeding them in the early phases of their life.

Learn to make peace with your detritus! As always, look to the wild aquatic habitats of the world for an example of how this food source functions within the greater biome.

I'm fascinated by the "mental adjustments" that we need to make to accept the aesthetic and the processes of natural decay, fungal growth, the appearance of biofilms, and how these affect what's occurring in the aquarium. It's all a complex synergy of life and aesthetic, and once we grasp what's happening in our tanks, we can truly understand how important it all is.

And realizing that this accumulation of biological material can all provide a certain something- in this case,  ecological continuity- for your aquarium in many iterations and phases of its existence is of profound importance. This is an invaluable asset provided to us free of charge by Nature, ready for use...if we allow it to remain in our tanks.

Our entire approach is about creating a biome- a little closed ecosystem, which requires us to support the organisms which comprise it- at every level.

Just like what Nature has been doing for eons.

Stay consistent. Stay observant. Stay curious. Stay diligent. Stay patient...

And Stay Wet.


Scott Fellman

Tannin Aquatics


Scott Fellman
Scott Fellman


Leave a comment