Remember when you were back in elementary school, and your class would take a "field trip" to a museum or some place like that, and you had to get a "permission slip" signed by your mom or dad? It was like the "golden ticket!" A license to voyage beyond the normal confines of the classroom, or even the playground! I remember how good it felt; how empowering- to have that signed permission slip and to be able to go on that excursion to some interesting and exciting place.

I think we all can relate to that, right?

Flash forward a few decades, and it seems like many of us in the aquarium hobby are still looking for that "permission slip"- albeit a metaphorical one- to venture outside of the boundaries of what is considered "acceptable" or "normal" aquarium practice. I routinely receive emails from fellow hobbyists asking me if it's okay to attempt certain things in a botanical-style aquarium. It's interesting and a bit funny that people ask me these questions- as if I'm some "authority figure" who needs to "sign off" on everyone's botanical-style aquarium experiments.

I'm not, of course. However, I am honored to be considered as a source of advice for this kind of stuff. Like many of you, I've played with this stuff for many years, and I've had a lot of experiences-mostly good, but some not-so-good- with these types of experiments. And it's not like me or anyone else has to give you "permission" to go for it.

On the other hand, I'm proud that both myself and many members of our community are boldly trying some new ideas that certainly fly in the face of "conventional aquarium wisdom" and practice, and have yielded interesting benefits for our fishes. And, humans being humans, we like the "approval" of our peers to try stuff previously viewed as "taboo."


I thought it might be fun to look at a few of the things which we as hobbyists previously felt a bit scared to attempt, but now, thanks to the hard work of our community, feel that we collectively now have "permission" to proceed with! Let's get right to 'em:

Fungal growths and biofilms are okay to have in your aquarium. Yeah, the idea of seeing these stringy, gooey-looking growths on our leaves and botanicals and wood can certainly cause concern for many hobbyists. The rapidity with which it grows and proliferates can be downright frightening for the uninformed hobbyist. A century of aquarium hobby practice and thought leadership by experts has told us this is really BAD! Get it out- like, immediately.

Yet, this is a mandate that we have followed dutifully for generations without thinking about the upsides to this stuff.

We have to look at how these growths occur and benefit aquatic habitats in Nature.

When leaves enter tropical streams and other bodies of water, fungal colonization causes leaves to increase nitrogen content (because of fungal biomass) and leaf maceration. This is known by aquatic ecologists to be evidence of microbial colonization. There are many different stages in the process, starting with the leaching of materials from the cells of the botanicals during initial submersion, in which soluble carbon compounds are liberated in the process. A rapid release of phosphorus accompanies this leaching.

Of course, the process ultimately leads to physical breakdown and/or fragmentation of the leaves and botanicals into smaller "pieces", which possess larger amounts of surface area for microbial attachment.  Extensive ecological studies done by scientists specifically in regard to leaf litter have yielded a lot of information about this process.

The fungi known as aquatic hyphomycetes produce enzymes which cause leaf maceration, and in as little as 2 to 3 weeks, as much as 15% of the decomposing leaf biomass in many aquatic habitats is processed by fungi, according to one study I found.

Now, sure, there could be a downside to having all of this growth in your tank...and it has to do both with the prolific nature of fungi and the impatience of us as hobbyists. We need to consider the fact fungal colonization facilitates the access of invertebrates to the energy trapped in deciduous leaves and other botanical materials found in the aquatic environment. Bacteria and fungi that decompose decaying plant material in turn consume dissolved oxygen for respiration during the process.

This is why adding too much botanical material too rapidly to an aquarium can create problems for the fishes! A rapid decrease in dissolved oxygen in a small body of water can be disastrous; or, at the very least, leave fishes gasping at the surface! And of course, that's why we tell you to deploy massive patience and to go slowly when adding botanicals to an established aquarium...

Of course, that's the worst case scenario- precipitated by us as impatient hobbyists adding too much stuff to an established aquarium too quickly. It's common sense. However, when we employ patience and allow fungal growths and biofilms to grow and proliferate, we can benefit our aquariums in ways previous generations of aquarists haven't considered.

These growths serve as a "medium" upon which other food sources accumulate and reproduce.

In the wild tropical leaf-litter-fueled ecosystems we love so much, creatures like hydracarines (mites), insects, like chironomids (hello, blood worms!), and copepods, like Daphnia, are the dominant fauna that fishes tend to feed on.  Thes organisms feed directly on biofilms, fungal growths, and the leaves themselves.

Gut content analysis of fishes which inhabit leaf litter habitats reveals a lot of interesting things about what our fishes consume.

For one thing, in addition to the above-referenced organisms, organic detritus, fungal growths, and "undefined plant materials" are not uncommon in the diets of all sorts of fishes.This is interesting to contemplate when we consider what to feed our fishes in aquariums, isn't it?

Again, just think about it: These life forms, both planktonic and insect, tend to feed off of the leaf litter itself, as well as fungi and bacteria present in them as they decompose...Just like the fishes that are found there. And of course, this "interconnectivity" between various levels of life forms creates the basis for a fascinating and surprisingly productive "food web."

Food webs, defined as "a system of interlocking and interdependent food chains" are fascinating constructs in Nature. The leaf litter bed is a surprisingly dynamic, and one might even say "rich" little benthic biotope, contained within the otherwise "impoverished" blackwaters which surround it. 

And, as we've discussed before on these pages, it should come as no surprise that a large and surprisingly diverse assemblage of fishes make their homes within and closely adjacent to, these litter beds. These are little "food oases" in areas otherwise relatively devoid of food.

 It works the same way in our aquariums.

Allowing botanicals and leaves to fully break down in the aquairum. As we've discussed for years here, leaving leaves and botanicals in our aquairums to fully decompose does not have a detrimental impact on water quality in otherwise well-managed systems.

Pieces of leaves and botanicals fall to the bottom of the aquairum, and form a bed of…detritus. Yes, I said detritus. In the aquarium world, we've long vilified the stuff as “a destroyer of water quality”; an impediment to successful aquariums. And the reality is that, in a well-managed aquarium, "detritus" is an essential food source for many organisms and plants. 

Like anything else in a closed system, if it's not allowed to accumulate unchecked to the point of creating a real mess in the tank, I personally believe its benefits for the animals we keep far outweigh any perceived disadvantages of having it present.

I know that uneaten food and fish poop, accumulating in a closed system can be problematic if overall husbandry issues are not attended to. I know that it can decompose, overwhelm the biological filtration capacity of the tank if left unchecked. And that can lead to a smelly, dirty-looking system with diminished water quality. I know that. You know that. In fact, pretty much everyone in the fucking hobby knows that.

That's not the issue, really, IMHO.

The "issue" is that we as a hobby have sort of heaped detritus into this "catch-all" descriptor which has an overall "bad" connotation to it. Like, anything which is allowed to break down in the tank and accumulate is bad.

I'm not buying it.

Why is this necessarily a "bad" thing?

Check out he definition of detritus: 

"detritus is dead particulate organic matter. It typically includes the bodies or fragments of dead organisms, as well as fecal material. Detritus is typically colonized by communities of microorganisms which act to decompose or remineralize the material." (Source: The Aquarium Wiki)

I mean, even in the above the definition, there is the part about being "colonized by communities of microorganisms which act to decompose or remineralize…"


It's being processed. Utilized. What do these microorganisms do? They eat it...They render it inert. And in the process, they contribute to the biological diversity and arguably even the stability of the system. Some of them are utilized as food by other creatures. Important in a closed system, I should think.


It's not all bad, right?

And it's fueled by stuff like decomposing leaves and botanicals.

So, yeah- I let my leaves and botanicals stay in my aquariums until they completely break down, only removing them if they become an annoyance (ie; every time a fish moves, a pile of the shit gets stirred up, or its accumulating on my driftwood, etc.)- but it never gets to that point in my tanks.


It's not an excuse for sloppy husbandry, or neglecting the removal of offensive materials. However, it IS a sort of acceptance of the fact that "stuff happens" in nature- and in aquariums- and that many of these things are simply not worth getting upset about. I mean, if you have an aquarium with brown water, and substrate dominated by decomposing leaves and softening botanicals, it shouldn't come as any surprise, right?

Decomposition is not something to freak out about. Rather, it's something to celebrate. Life, in all of its diversity and beauty, still needs a stage upon which to perform...and you're helping provide it, even with material changes taking place daily.

The real the key here is that pace- and an understanding that the materials that we add need to be added-and replaced- at a pace that makes sense for your specific system. An understanding that you'll have a front row seat to the natural processes of decomposition, transformation, decay...and accepting that they are part of the beauty of this style of aquarium, just like they are in Nature.

Mixing botanical materials into your substrate. We've been talking about the idea of "substrate enrichment" and utilizing alternative materials to create "active" botanical substrates I the aquarium for over 5 years now. We've. been doing this ourselves for a long time with nothing but good results.


One of the things that many hobbyists ponder when we contemplate creating 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 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, I base this on visual inspection of numerous tanks, and the basic chemical tests I've run on my systems under a variety of circumstances.

The understanding that substrate in the aquarium can be more than just sand or gravel- and, indeed- should be in many circumstances- is to me one of the great advances in our hobby. When we consider that almost all aquatic habitats are influences by the surrounding terrestrial environment, it's simply head-scratching to me that we haven't played with this idea for years and years I the aquarium hobby.

You can have tinted, even turbid water without it being "dirty"   In the aquarium, the hobby at large tends to see colored water, or water with some turbidity to it, and think..."dirty." 

It's head scratching to me how this came to be. And it's a HUGE "thing" when we hear criticisms and concerns from other parts of the aquarium world about our work.  There's a lot of confusion and misunderstanding at play here...and a lot of commentary from people who just don't understand this stuff all tat well.

And of course, this is where we need to separate two factors:

Turbidity (generically referred to as "cloudiness") and "color" are generally separate issues for most hobbyists, but they both seem to cause concern. Cloudiness, in particular, may be a "tip off" to some other issues in the aquarium. And, as we all know, cloudiness can usually be caused by a few factors:

1) Improperly cleaned substrate or decorative materials, such as driftwood, etc. (creating a "haze" of micro-sized dust particles, which float in the water column).

2) Bacterial blooms (typically caused by a heavy bioload in a system not capable of handling it. Ie; a new tank with a filter that is not fully established and a full compliment of livestock).

3) Algae blooms which can both cloud AND color the water (usually caused by excessive nutrients and too much light for a given system).

4) Poor husbandry, which results in heavy decomposition, and more bacterial blooms and biological waste affecting water clarity. This is, of course, a rather urgent matter to be attended to, as there are possible serious consequences to the life in your system.

And, curiously enough, the "remedy" for "cloudy" water in virtually every situation is similar: Water changes, use of chemical filtration media (activated carbon, etc.), reduced light (in the case of algal blooms), improved husbandry techniques (i.e.; better feeding practices and more frequent maintenance), and, perhaps most important- the passage of time.

There are of course, other factors that affect clarity, like fishes that dig or otherwise disturb the substrate and wood with their grazing activities, but these are not necessarily indicative of husbandry issues.

Okay, that was "Aquarium Keeping 101", actually.

Although we all seem to know this, I hear enough comments and questions about the color of the water and its relation to "cleanliness" in  natural, botanical-style blackwater systems that it warranted this seemingly "remedial" review!

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

People ask me a lot if botanicals create "cloudy water" in their aquariums, and I have to give the responsible answer- yes. Of course they can!

If you place a large quantity of just about anything that can decompose in water, the potential for cloudy water caused by a bloom of bacteria exists. The reality is, if you don't add 3 pounds of botanicals to your 20 gallon tank, you're not likely to see such a bloom. It's about logic, common sense, and going slowly.

Remember, too, that some "turbidity" in the water, in either a "whitewater" or "blackwater" system, is natural,expected, and not indicative of a problem. In many natural settings, water is chemically perfect but not entirely "crystal clear."  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.

In my home aquariums, and in many of the really great natural-looking blackwater aquariums I see the water is dark, almost turbid or "soupy" as one of my fellow blackwater/botanical-style aquarium geeks refers to it. You might see the faintest hint of "stuff" in the water...perhaps a bit of fines from leaves breaking down, some dislodged biofilms, pieces of leaves, etc. Just like in nature. Chemically, it has undetectable nitrate and phosphate..."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?

"Turbidity." Sounds like something we want to avoid, right? Sounds dangerous...

On the other hand, "turbidity", as it's typically defined, leaves open the possibility that it's not a negative thing:

 "...the cloudiness or haziness of a fluid caused by large numbers of individual particles that are generally invisible to the naked eye, similar to smoke in air..."  

What am I getting at?


Well, think about a body of water like an igapo adjacent to the Rio Negro, as pictured above in the photo by Mike Tuccinardi. This water is of course, "tinted" because of the dissolved tannins and humic substances that are present due to decaying botanical materials.  And it's also a bit "turbid" because of the fine particulate matter from these materials, too.

In summary- tinted, turbid water and high water quality are not mutually exclusive. You can have these and have excellent water quality. I know, because most of my tanks look like that, and have water quality on par with most reef systems I've kept over the years.

In the end, you don't need my "permission"- or anyone's- to try new things; to push the boundaries out into unconventional practices. The natural, botanical-style aquarium is so interesting to me because it offers enormous opportunity to execute aquariums based on the function of natural habitats- functions which, although they may look different than anything we've ever done before, may just unlock the keys to many new aquarium discoveries.

What I can promise to you in 2021 and beyond is that we will continue to provide products, ideas, and inspiration to give you the tolls you need- and hopefully, the confidence- to move forward boldly, to unlock all sorts of exciting aquarium-related things. So, you do have my have FUN!

Stay excited. Stay bold. Stay creative. Stay curious. Stay intrigued...

And Stay Wet.


Scott Fellman

Tannin Aquatics 

Scott Fellman
Scott Fellman


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