The whole picture...

One of the interesting things about creating a botanical method aquarium is that it's really easy to get "into the weeds" about the ecology and the environmental aspects of the tank, almost at the exclusion of everything else. We tend to emphasize the function of the ecosystem that we are developing over almost all else. And sometimes, I admit, that can be a bit short-sided. 

Sometimes, it's important for me as a self-proclaimed "thought leader" in this space to delve into the more practical, everyday, or even mundane aspects of their management. Let's talk about a few of these things today, in no particular order...


For all of the hobbyists who have simply come to expect that the water in their tanks will typically never be crystal clear, we still receive a fair number of questions asking if it's "normal" for the water to have a slight "hazy" look to it (in addition to the color, of course).

The water is almost never perfectly crystal clear in our botanical method aquariums. The clarity of the water in our aquariums is directly related to the physical dissolution of "stuff" in the water, and is influenced-and mitigated by- a wide-range of factors. Turbidity ( defined as "..the quality of being cloudy, opaque, or thick with suspended matter") is completely normal and common in the botanical method aquarium.

I won't disagree that "crystal-clear" water is nice. I like it, too...However, I would make the case that "crystal-clear" water is: a) not always solely indicative of "healthy" or "optimum" , and b) not always what fishes encounter in Nature. 

Habitats such as flooded forests are almost never crystal clear. The large quantity of soil, sediments, and decomposing vegetation that is present on the forest floor during the dry periods will often create turbid conditions that will linger throughout the phase of inundation.


Botanical materials will impact the clarity of the water as they begin to decompose and impart the lignin, tannins, and other compounds from their physical structure into the water in our aquariums. Also, many of us use alternative substrate materials, consisting of bits of botanicals, sediments, and clays- and these will also have a definite impact on the clarity of the water. There will always be small amounts of this stuff in suspension.

Remember, just because the water in a botanical-influenced aquarium system is brownish, and even slightly hazy, it doesn't mean that it's of low quality, or "dirty", as we're inclined to say. It simply means that tannins, humic and fulvic acids, and other compounds from the botanical materials are leaching into the water, creating a characteristic color and turbidity that some of us geeks find rather attractive. If you're still concerned, monitor the water quality...perform a nitrate or phosphate test; look at the health of your animals.

These factors will tell the true story.

You always need to ask yourself, "What's actually happening in there?"

In almost every case in my experience, chemically, the water has minimally detectable concentrations nitrate and phosphate...biologically"clean" by aquarium standards.

Sure, by municipal drinking water standards, color and clarity are important, and can indicate a number of potential issues...But we're not talking about drinking water here, are we?

I believe that a lot of what we perceive to be "normal" in aquarium keeping is based upon artificial "standards" that we've imposed on ourselves over a century of modern aquarium keeping. Everyone expects water to be as clear and colorless as air, so any deviation from this "norm" is cause for concern among many hobbyists.

It need not be, IMHO.


To your comfort, you'll find that botanical method aquariums are as stable as any other if you follow regular maintenance and good old common sense.

So, what are we talking about, in regards to "regular maintenance?"

Well, for one thing, water exchanges. Yes, the dreaded freakin' water exchanges...Because the topic is so well discussed in the aquarium world,  I'll keep it relatively brief on this topic: 

What’s a good water-exchanging regimen?

I’d love to see you employ 10% per week...It’s what I’ve done for decades, and it’s served me- and my animals- very well! Regardless of how frequently you exchange your water, or how much of it you exchange- just do them consistently. And of course, as previously discussed, don't go crazy siphoning every bit of detritus out during the process.

Remember that, in an aquarium which encourages the growth of bacteria, fungi, copepods, etc., the organic material contained in detritus becomes part of the "food web." And everybody up the food chain can benefit from the stuff.

So, by going "full ham" and siphoning out every last speck of detritus from your tank, you're essentially breaking this chain, and denying organisms at multiple levels the chance to benefit from it! Yeah, over-zealously siphoning this material from your tank effectively destroys an established community of microorganisms which serve to maintain high water quality in the closed environment of an aquarium!

This is a super-important point to remember!

In an ironic twist, I believe that it's far more common for those "anomalous" ammonia spikes and such that aquarists report periodically, to have their origin in over-zealous cleaning of aquariums and filter media, as opposed to the accumulation of detritus itself. So, yeah-taking out all of the "fish shit" is actually removing a complex microbiome that's keeping your tank healthy!

Even something as seemingly "mundane" as the way we maintain our botanical-method aquariums requires us to make some "mental shifts" to appreciate our methodology more thoroughly, doesn't it?


Well, some of it does...It's almost inevitable that some stuff gets shifted around. Leaves and seed pods are pretty lightweight materials, and as they decompose, they're even more lightweight and "mobile."

And that's not necessarily a bad thing. Don't get stressed if you stir some stuff up. Your tank will be fine. Likely, the fishes couldn't care less...

Think about the natural leaf litter beds, and the processes which influence their composition, structure, and resilience. Many litter beds are long-term "static" features in their natural habitats. Almost like reefs in the ocean, actually. Yet, there is a fair amount of material being shifted around constantly by current, rain, flooding, and the activities of fishes.

Yeah, stuff does get disturbed and redistributed.

The organisms which reside in these systems deal with these dynamics effectively. They have for eons.

The benthic microfauna which our fishes tend to feed on also are affected by this phenomenon. And as mentioned above, the fishes tend to "follow the food", making this a case of the fishes learning (?) to adapt to a changing environment.

And perhaps...maybe...the idea of fishes sort of having to constantly adjust to a changing physical (note I didn't say "chemical") environment could be some sort of "trigger", hidden deep in their genetic code, that perhaps stimulates overall health, immunity or spawning?

Something in their "programing" that says, "You're at home...the season has changed, because there's an influx of new water...leaves are rolling around..." Perhaps not as "specific", but something like that, which can trigger specific adaptive behaviors?

I find this possibility fascinating, because we can learn more about our fishes' behaviors, and create really interesting habitats for them, simply by adding botanicals to our aquariums and allowing them to "do their own thing"- to break apart as they decompose, move about as we change water or conduct maintenance activities, or to be added to from time to time.

Which leads us to the next, most commonly-asked question about maintaining botanical method aquairums:


Hell, yes.

Take care of your aquarium- your miniature closed ecosystem-by taking care of the enormous microcosm which supports its form and function. And that means, not removing all of this material as it decomposes. I know, I've said it several times already in this one piece, and countless times in "The Tint" and elsewhere, but it's really a fundamental part of the botanical method of aquarium keeping.

Of course, I realize that the aquarium is a microcosm of Nature, and not an open system. However, in principle, many of the factors which control Nature control our aquariums, too. Some are a bit different in "execution", but the influence is similar. 

I don't do a lot of siphoning of decomposing botanicals from my substrates, which are typically a mish-mash of leaves, twigs, and bits and pieces of botanicals. Sure, you CAN stir up this layer, and simply "swish" a fine meshed net around in the water column, and try to remove anything you find offensive.

I wouldn't get too carried away with it. Other than from an aseptic standpoint, I have a hard time justifying the removal of decomposing botanicals from the aquarium to any great extent. 

What goes down...doesn't always have to come up!

This is not an excuse to develop or accept lax maintenance practices. It's simply a "call to awareness" that there is probably nothing wrong with your system when you see this stuff. It's quite contrary to the way we've been "acculturated" to evaluate the aesthetics of a typical aquarium. You'll have to get used to a certain amount of material decomposing in your tank.

It's perfectly natural, and part of the function of the aquarium...and, in a more superficial sense- part of the aesthetic. Accepting the fact that you'll see decomposing materials, biofilms and fungal growth in your system is something that many aquarists have a very difficult time with.  I get it. Again, it's one of those things that many of us are simply not accustomed to in our aquarium keeping work.

Observe underwater videos and photos of environments such as the Amazonian region, etc. and you'll see that your tank is a much closer aesthetic approximation of nature than almost any other system you've worked with before!

And, to your comfort, you'll find that these systems are as "chemically clean" as any other if you follow regular maintenance and common sense. 

Ultimately, your decision to create a botanical method aquarium is as much a philosophical one as it is a practical one. To accept nature, rather than to fight it, is a bit at odds with the mindset many of us have with regards to aquarium keeping.

As you begin to understand and evaluate your own aquarium, you'll gain a greater appreciation for the wonders of Nature, and the processes that have occurred for eons. And of course, you're going to really appreciate the "whole picture" of seeing your aquarium function and appear much like a natural aquatic ecosystem does.

It's something that's truly transformative in our hobby; something which only those who dare to be different can experience.

Stay Bold. Stay Creative. Stay excited. Stay diligent...

And Stay Wet.


Scott Fellman

Tannin Aquatics 



Scott Fellman
Scott Fellman


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