Understanding the "biological operating system" of your aquarium

With so many people coming into the botanical-style aquarium world from all different sectors in the hobby, it's a given that we receive more questions about things which many of us who have been "in the game" for a while might take for granted.

Yet, it's important NOT to take anything for granted, and to consider all the possibilities, reasons, and ideas for managing our systems.

Apart from, "What botanicals should I use for a _____________ style setup?" the most common question we receive is ""Do I leave them in or let them break down in my tank?"

And of course, our simple answer is..."It's your call!"

Now, this is an important question. How we answer it- work with it- has fundamental implications for how we operate our blackwater, botanical-style aquariums.

It's as much about your aesthetic preferences as it is about the long-term health of the aquarium. It's a decision that each of us makes based on our tastes, management "style", and how much of a "mental shift" we've made into excepting the transient nature of a blackwater, botanical-style aquarium and its function. There really is no "right" or "wrong" answer here. It's all about how much you enjoy what happens in nature versus what you can control in your tank.

I tend to favor nature. But that's just me.

I like the idea of leaving materials in my aquariums until they break down completely. Long, long ago, I made that mental shift to a philosophy which says, "Hey, it's okay to have some decomposing stuff and biofilms and...detritus...in your tank. It's natural-looking!"

Now, the caveat here is that I didn't just "give myself permission" to neglect tanks or avoid basic husbandry...no, that wasn't the point. The point is to accept that materials breaking down in our aquariums can provide "fuel" for the biological processes which create long-term stability in a closed system. 

Like any other type of aquarium, a botanical-style system relies on time-honored practices of maintenance, nutrient export, and attention from the aquarist. However, one thing that we have that a lot of types of systems don't is an abundance of potential food sources for a myriad of organisms which reside in our tanks. We are very much creating a little microcosm, and it needs to respect the "checks and balances" which Nature imposes.

And of course, we can't ever lose sight of the fact that we are creating and adding to a closed aquatic ecosystem, and that our actions in how we manage our tanks must map to our ambitions, tastes, and the "regulations" that Nature imposes upon us.

She'll kick your ass if you don't pay attention.

Personally, I don't mind the "look" of a tank with decomposing leaves and botanicals. Where some might see "dirty", I see "natural." I see the ultimate expression of ephemeral and the living embodiment of "wabi-sabi"- an acceptance of the beauty of transience. And I don't think my tanks look that "dirty".

Like most aquarists how play the botanical-style aquarium game, I do understand that aquariums have some limitations to how hard you can push them...

Everything that you add into your aquarium that begins to break down is bioload. That's a fundamental consideration that we have to put in our heads. It's not "good" or "bad"- it's simply a consideration.

Everything that imparts proteins, organics, tannins, etc. into the water is something that you need to consider. However, it's always been my personal experience and opinion that, in an otherwise well-maintained aquarium, with regular attention to husbandry, stocking, and maintenance, the "burden" of botanicals in your water is surprisingly insignificant.

And these systems are remarkably stable once established.

Even in test systems where I intentionally "neglected" them by conducting sporadic water exchanges, once I hit my preferred "population" of botanicals (by building them up gradually), I have never noticed significant phosphate or nitrate increases that could be attributed to their presence. Those biological "yardsticks" for water quality are pretty significant, IMHO.

It's also important to consider that the breakdown of botanical materials, if left in your system, can be utilized by animals and plants. Yep, this is particularly important in the context of planted botanical-style/blackwater aquariums! 

Allowing plants, fishes, shrimp, and bacteria the chance to utilize the decomposing botanicals in their life cycle is an important part of the game, IMHO. Being overly fastidious about siphoning out every speck of dirt or botanical material as it breaks down is "overkill", in my opinion, and can be just as detrimental as over-doing things. 

Nature strikes a balance. Nature thrives on efficiency. When you're adding botanicals to a tank, you're not just doing "aquascaping"- you're laying down the groundwork for the "biological operating system" of your aquarium. As such, you need to think "big picture" here. (That "functional aesthetics" thing again!)

And while we're talking about adding botanicals, from time to time, I need to revisit the "doomsday scenarios" that could occur. Now, it's important to note that the very few "disasters" we've been told about typically happened under a few situations or combinations of them:

1) The aquarist did not prepare anything as instructed

2) A significant amount of botanicals relative to water volume was added all at once to a long-established aquarium

3) A significant amount of botanicals was added to an established tank in a very short period of time (like within a few days)

Now, again, there are always anomalies, but these situations are almost "set ups" for some types of issues. Typically, what happens is you'd see fishes gasping at the surface for oxygen, which becomes rapidly depleted by the addition of a large influx of materials breaking down, which can also overwhelm the biological filtration capacity of a tank. 

Usually, the "rescue" consists of increased vigorous aeration and a succession of water changes, removing the botanicals, use of activated carbon, etc...the typical "emergency fixes" for problems of this nature.

The best preventative is to go slowly. To consider impacts.

The reality is, adding botanicals to your tank and using them, replacing them regularly, etc, is no more "dangerous" than anything else we do as aquarists. You simply need to go slowly, apply common sense, follow our prep instructions, and observe your tank carefully.

Is that a guarantee of success? Of course not. Could you have some weird combination of events, local water composition, overly sensitive fishes, etc. which could give you a disastrous outcome? Of course. 

Look, stuff can still occasionally go wrong, even when you follow instructions and employ common sense. Aquariums are closed natural ecosystems, and changing the delicate balance within them always risks disrupting established biological processes. Just like using additives, CO2, or other regimens in our tanks, when we "invade" the actual processes, stuff that we don't anticipate can happen.

It's the reality of Nature, and a reminder that, although we can control some things, Mother Nature calls the shots...We are treading on Her turf, and we have to understand that there are no guarantees for success "just because."

She owes us nothing. 

It's not a bad thing. It's just...reality.

Now, all that doom and gloom and "reality checking" being said, Nature PROVIDES us with something. For free.



Yeah, detritus. Produced by the "processed" and decomposing plant matter, detritus, is considered by many aquatic ecologists to be an extremely significant food source for many fishes, especially in areas such as Amazonia and Southeast Asia, where the detritus is considered an essential factor in the food webs of these habitats.

And of course, if you observe the behavior of many of your fishes in the aquarium, such as characins, cyprinids, Loricarids, and others, you'll see that in between feedings, they'll spend an awful lot of time picking at "stuff" on the bottom of the tank. In a botanical style aquarium, this is a pretty common occurrence, and I believe an important benefit of this type of system. 

I am of the opinion that a botanical-style 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 organisms within it can provide an excellent supplemental food source for our fishes!

The dynamic of input and utilization of materials from the surrounding forest habitats is fascinating and profound for those of us who wish to mimic these habitats in our aquariums... And we can, to a certain extent, by utilizing botanicals as part of our aquarium's "operating system."

Nature offers us abundance, challenges, guidelines, and hard and fast "rules." How we choose to work with them is our choice, our decision, and our privilege.

Stay curious. Stay inspired. Stay bold. Stay diligent. Stay undaunted...

And Stay Wet.


Scott Fellman

Tannin Aquatics 






Scott Fellman
Scott Fellman


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