Filtration and the Botanical-Style Aquarium...

When we were first indoctrinated into the aquarium hobby, we were typically advised to purchase an aquarium, a heater, and a filter...

A "filter." 


One of the more "basic" components of an aquarium is filtration. And with filtration, you have the collateral effect of water movement in the aquarium. This is a topic to which we as aquarists typically give modest amounts of thought, other than determining what type/size of filter to use in our tank. Then, it's on to sexier topics, like "Which piece of Manzanita do I use...?" 

We spend a great deal of time contemplating the look and feel of our botanical-syle aquariums, and wrapping our head around the various "mental shifts" necessary to really appreciate and embrace this approach...You know- learning not to fear the tinted water, decomposing botanical materials, biofilm, detritus, etc.- all that stuff.

And that's really great. It's foundational.

However, I must admit that another one of the "foundational" things we don't talk about as much as we should is filtration. We receive a surprisingly large number of questions on the topic.

Yeah, the ubiquitous, necessary, and highly important function of filtration in our aquariums is definitely something we, as lovers of leaves and botanicals, need to give a little thought to when we set up our systems. 


The reality is that, in a botanical-style natural aquarium, filtration and water movement are influential and pretty important in the grand scheme of things. As with any aquarium, it's important to apply filtration that keeps up with the specific needs of your tank and its inhabitants. Of course, with the heavily botanical-influenced aquarium, there is the added consideration of all of those leaves and pods and such.

These items not only are part of the "hardscape"- their ephemeral nature makes them a component of the bioload of the system- and due consideration needs to be paid to their impact on the closed system's environment. Remember, leaves, seed pods, and the like are "ephemeral"in many respects, slowly decomposing and breaking down, releasing not only "bits and pieces", but organic materials as well. 

That's where filtration comes in.

Now, Nature provides Her own form of "filtration" in the form of the nitrogen cycle and the bacteria which accompany it. Bacterial biofilms- the bane of many a new aquarist- are actually a true benefit because of what they are comprised of (bacteria, hello!), and for the potential supplemental food source they become...Oh, I"m digressing, yes. And of course, fungal growth on the botanicals also serves to physically break down and "process" some of the botanical materials and their accompanying organics from the water column.


Now, I'm no filter "expert." I'm not an aquarium "gearhead."  In fact, I really don't care much for the gear. It neither excites me or stimulates ideas for me. I mean, I DO like reef gear, but overall, it's not my hobby obsession. I view it as something necessary to operate an aquarium.

Shit, Sounds like I'm the PERFECT guy to write a piece on filters, right? My thoughts on this topic are based, like everything I write- on my personal experience and ideas, laced with a healthy dose of "opinions" and stubbornness... 🤔

So, here's the "long and the short" of this topic:

You can use just about any type of filter available in the hobby on your botanical-style blackwater/brackish aquarium.

The real considerations, IMHO, are: A) where in the water column you are bringing in water, and b) Where the outputs are aimed. Oh, and C) what media you're using in the filter.

So, let's look a bit closer. 

I have used all sorts of filter systems on my BWBS style systems over the years, but the ones that I tend to use will surprise you...maybe. Maybe not.

As a reefer, I love my tanks with built in overflows and sumps.

I love sumps.

I love them because:

a) You don't see any of the ugly shit (heaters, etc.) in the tank proper. Oh, and even that damn "glassware"- yes, I know that YOU may not think they're ugly, but I'm no fan of them as they are now. They completely and utterly suck in every way, in my humble opinion. I hate them. Why? We can have that discussion some other time, okay?😳

b) Sumps add water volume to your tank. As the sayings goes, "Dilution is the solution to pollution"- and stability! 

c) Sumps provide an area where you can keep filter media, biological media, botanicals, wood, etc. to influence environmental conditions in the display aquarium. Like, if you just hate the look of leaves and decomposing stuff in your display, but love the blackwater look and biodiversity, sumps are a good choice. No, actually- they're a great choice!

d) They rely on surface overflow "weirs" to supply water. Overflow weirs skim water from the surface, removing the film which accumulates and can interfere with gas exchange...Important when you have lots of botanicals in your tank breaking down, right?

So-called "all-in-one" tanks, like my Innovative Marine "Fusion Lagoon" system, or my Ultum Nature Systems AIOs, offer a great "hybrid" of a "sump" (in this case, a rear-mounted external filter compartment) and an external filter, making an affordable, simple, aesthetically clean, easy-to-maintain-and-operate system.

Now, I realize that not everyone wants the expense, logistics, challenges, and additional considerations (return pumps, space under the tank, etc.) which go along with the use of sumps. I also realize that the majority of freshwater hobbyists utilize glass aquariums without overflows and such, so there are numerous other options.

And of course you can employ those ubiquitous, ever-popular canister filters!


Shit, canister filters necessitate the need for glassware, right? Arrghhhh.... 

IMHO, you should direct the return from canister filters near the surface, to create agitation and to facilitate gas exchange. Unlike pure planted aquariums, where there is a definite benefit from using those damn "Lily Pipes" and such to return water well below the surface to preserve CO2, I personally believe that heavily-stocked botanical-style aquariums benefit from this surface agitation.

Oh, did I mention that I hate those pipes? Just wanted to make sure on more time...

To be clear- I hate them...😆

And yeah, I've broken a bunch over the years...

You can return some of the water towards the lower levels of the tank to keep things "stirred up" just a bit, without blowing shit all over the tank. (that's a technical term, by the way).

And of course, outside power filters do the same thing- keep everything relatively neat and tidy, and potentially outside of the tank if you like.

Oh, and sponge filters are great- and those so-called "Matten Filters", too- because they are primarily biological filters and are relatively easy to hide in displays...

Now, I have spent a fair amount of time alleviating the fears of you weirdos who don't want to see leaves and pods and such in your tank physically by explaining that you can just toss these things into your filter or sump! And of course, it goes without saying that you can utilize all of these filters with the botanicals present in the display, as well, of course.

Like, duh.

The real "issue", if you want to call it that- with filtration in regards to our botanical-style aquariums is what media you utilize. Again, I call on my reef-keeping experience to tell you that I am a huge fan of activated carbon. I use it on every tank I set up- even the ones with the gnarliest (yes, it's a word- I'm from L.A.-we talk that way. It's a word. Deal with it.), darkest "tint"  imaginable. 

I love activated carbon.


"Carbon? WTF Fellman?"

Yes, carbon can remove some of the tint and probably even some of the valued humic substances and other beneficial compounds exuded by botanicals. It's not selective. That being said, it also can remove impurities, like volatile dissolved organic compounds, urea, some metals, etc. It's valuable stuff.

The key is to just not overdo it.

Of course, if you want leaves and such in your tank, but not the tint- as we've discussed many times- just use the 'recommendedl" dose of carbon and you have the best of both worlds- at least, aesthetically.

Better as chemical filtration media would be stuff like specialized ion-exchnage or "organic scavenger resins" and zeolites- stuff which requires more research, trial and error, and testing. But it is possible, at least in theory, to incorporate filtration media which removes the undesirable pollutants and retains the desired humic substances and tannins. Oh, and proper biological function in low pH systems, fostering the "biome" of these tanks.

I like the"Poly Filter" pad, by Poly BioMarine, as it removes organics and can remove stuff like ammonia even in low pH systems. In my years of working with this stuff, I have not seen it remove substantial amounts of the "tint" in the water caused by tannins from botanicals. This is hardly a scientific assessment of the stuff, but I believe in it. I've used it for decades in pretty much every type of aquarium- fresh, brackish, reef- that I've maintained with excellent results. 

And back to those "specialized resins" and such...

These things are are all something we will see more of in the me. There are numerous materials out there, used in other water purification work , that will definitely work with our aquariums.

In the mean time, you can continue use materials like carbon, Purigen, etc. to do the trick; just be aware of the way they work and what they will do. If you go "full power" (ie; the typical manufacturers' recommended "dose"), you'll have a really clear tank- if that's what you want.

Nonetheless, I adore Seachem Purigen.

It's a "macro-porous synthetic polymer" (aka "organic scavenging resin") that removes soluble and insoluble impurities from water by adsorption. In other words, it cleans up stuff.

Like, really well.

I think every aquarist should have Purigen in their "box of fish stuff...not just for regular use, but for...well...emergencies and stuff. It's really good stuff.

Yeah, you could use no filter, or just aeration, or even just employing a surface skimmer- and no other filter. The skimmer would facilitate gas exchange and provide some aeration.

The air/water interface is the "boundary" (technically called the "surface micro layer" by scientists) where all exchange occurs between the atmosphere and the aquatic environment. Interestingly, the The chemical, physical, and biological properties of the SML can differ significantly from the water just a few centimeters beneath the surface! 

In Nature, the concentration of these surface compounds depends on the source of the nutrients, as well as weather, like rain and wind. These organic compounds on the surface impact the the very physical and light admittance properties on the air/water interface. 

As aquarists, the biggest concern is that the surface film can interfere with gas exchange.

Oh, and it looks like shit, right? 

Or does it? I mean, we embrace turbid water and detritus and stuff, so why not accept some surface film? 

Well, we could. However, keep in mind the whole "gas exchange" thing. 

Now, you would have to obey the fundamental principles of aquarium management...water exchanges, proper stocking, careful feeding, etc. However, you can do this; I've done it many times.

We've especially done this with the "Urban Igapo" type of tanks, which rely on the biotia in the tank as a result of the substrate, vegetation, and botanicals. It's a throwback, if you will, to the earliest days of the aquarium hobby, when process and active management performed many of the same functions as filtration does today.


When we consider the aquarium itself as a living, breathing entity- one which has levels of life forms performing the biological "filtration" function, such bold experiments and concepts aren't all that weird, right?

This is a real "open source" component of what we do. An invitation and opportunity for YOU- the working aquarist- to make a big impact on the hobby, fostering benefits perhaps as yet not understood...

Is there one "best" filtration method?

Of course not.

So, yeah- use what works for you, benefits your fishes, and creates the best outcomes for them. There are so many approaches, any of which could work for you. 

The concept of filtration is constantly evolving. To me, besides the obvious benefits of utilizing media which can remove impurities and organics on a continuous basis from the aquarium, the most important ones are circulation and gas exchange/aeration.

The Botanical-Style Aquarium as The "Filter"

Okay, back to that thought we just hit on...

So, my thinking has been that you could actually use the tank itself and the botanical environment as the"biological filter", and simply use aeration/surface skimming and/or circulation pumps to facilitate the gas exchange. Not revolutionary, of course- but an idea that's often overlooked today.

The botanical materials present in our systems provide enormous surface area upon which beneficial bacterial biofilms and fungal growths can colonize. These life forms utilize the organic compounds present in the water as a nutritional source.

Oh, the part about the biofilms and fungal growths sounds familiar, doesn't it?

Let's talk about our buddies, the biofilms, just a bit more. One more time. Because nothing seems as contrary to many hobbyists than to sing the praises of these gooey-looking strands of bacterial goodness!

Structurally, biofilms are surprisingly strong structures, which offer their colonial members "on-board" nutritional sources, exchange of metabolites, protection, and cellular communication. They form extremely rapidly on just about any hard surface that is submerged in water.

When I see aquarium work in which biofilms are considered a "nuisance", and suggestions that it can be eliminated by "reducing nutrients" in the aquarium, I usually cringe. Mainly, because no matter what you do, biofilms are ubiquitous, and always present in our aquariums. We may not see the famous long, stringy "snot" of our nightmares, but the reality is that they're present in our tanks regardless.

The other reality is that biofilms are something that we as aquarists typically fear because of the way they look. In and of themselves, biofilms are not harmful to our fishes. They function not only as a means to sequester and process nutrients ( a "filter" of sorts?), they also represent a beneficial food source for fishes.

Now, look, I can see rare scenarios where massive amounts of biofilms (relative to the water volume of the aquarium) can consume significant quantities of oxygen and be problematic for the fishes which reside in your tank. These explosions in biofilm growth are usually the result of adding too much botanical material too quickly to the aquarium. They're excaserbated by insufficient oxygenation/circulation within the aquarium.

These are very unusual circumstances, resulting from a combination of missteps by the aquarist.

Typically, however, biofilms are far more beneficial that they are reven remotely detrimental to our aquariums.

Nutrients in the water column, even when in low concentrations, are delivered to the biofilm through the complex system of water channels, where they are adsorbed into the biofilm matrix, where they become available to the individual cells.  Some biologists feel that this efficient method of gathering energy might be a major evolutionary advantage for biofilms which live in particularly in turbulent ecosystems, like streams, (or aquariums, right?) with significant flow, where nutrient concentrations are typically lower and quite widely dispersed.

Biofilms have been used successfully in water/wastewater treatment for well over 100 years! In such filtration systems the filter medium (typically, sand) offers a tremendous amount of surface area for the microbes to attach to, and to feed upon the organic material in the water being treated. The formation of biofilms upon the "media" consume the undesirable organics in the water, effectively "filtering" it!

Biofilm acts as an adsorbent layer, in which organic materials and other nutrients are concentrated from the water column. As you might suspect, higher nutrient concentrations tend to produce biofilms that are thicker and denser than those grown in low nutrient concentrations.

Those biofilms which grow in higher flow environments, like streams, rivers, or areas exposed to wave action, tend to be denser in their morphology. These biofilms tend to form long, stringy filaments or "streamers",which point in the direction of the flow. These biofilms are characterized by characteristic known as  "viscoelasticity."This means that they are flexible, and stretch out significantly in higher flow rate environments, and contract once again when the velocity of the flow is reduced.

Okay, that's probably way more than you want to know about the physiology of biofilms! Regardless, it's important for us as botanical-style aquarists to have at least a rudimentary understanding of these often misunderstood, incredibly useful, and entirely under-appreciated life forms.

And the whole idea of facilitating a microbiome in our aquariums is predicated upon supplying a quantity of botanical materials- specifically, leaf litter, for the beneficial organisms to colonize and begin the decomposition process. An interesting study I found by Mehering, et. al (2014) on the nutrient sequestration caused by leaf litter yielded this interesting little passage:

"During leaf litter decomposition, microbial biomass and accumulated inorganic materials immobilize and retain nutrients, and therefore, both biotic and abiotic drivers may influence detrital nutrient content."

The study determined that leaves such as oak "immobilized" nitrogen. Generally thinking, it is thought that leaf litter acts as a "sink" for nutrients over time in aquatic ecosystems.

Oh, and one more thing about leaves and their resulting detritus in tropical streams: Ecologists strongly believe that microbial colonized detritus is a more palatable and nutritious food source for detritivores than uncolonized dead leaves. The microbial growth which occurs on the leaves and their resulting detritus increases the nutritional quality of leaf detritus, because the microbial biomass on the leaves is more digestible than the leaves themselves (because of lignin, etc.).

Okay, great. I've just talked about decomposing leaves and stuff for like the 11,000th time in "The Tint"; so...where does this leave us, in terms of how we want to run our aquariums?

Let's summarize:

1) Add a significant amount of leaf litter, twigs, and botanicals to your aquarium as part of the substrate.

2) Allow biofilms and fungal growths to proliferate.

3) Feed your fishes well. It's actually "feeding the aquarium!"

4) Don't go crazy siphoning out every bit of detritus.

Let's look at each of these points in a bit more detail.

First, make liberal use of leaf litter in your aquarium. I'd build up a layer anywhere from 1"-4" of leaves. Yeah, I know- that's a lot of leaves. Initially, you'll have a big old layer of leaves, recruiting biofilms and fungal growths on their surfaces. Ultimately, it will decompose, creating a sort of "mulch" on the bottom of your aquarium, rich in detritus, providing an excellent place for your fishes to forage among. 

Allow a fair amount of indirect circulation over the top of your leaf litter bed. This will ensure oxygenation, and allow the organisms within the litter bed to receive an influx of water (and thus, the dissolved organics they utilize). Sure, some of the leaves might blow around from time to time- just like what happens in Nature. It's no big deal- really!

The idea of allowing biofilms and fungal growths to colonize your leaves and botanicals, and to proliferate upon them simply needs to be accepted as fundamental to botanical-style aquarium keeping. These organisms, which comprise the biome of our aquariums, are the most important "components" of the ecosystems which our aquariums are.

It means adopting a different outlook, accepting a different, yet very beautiful aesthetic. It's about listening to Nature instead of the asshole on Instagram with the flashy, gadget-driven tank. It's not always fun at first for some, and it initially seems like you're somehow doing things wrong.

It's about faith. Faith in Mother Nature, who's been doing this stuff for eons.

It's about nuance.

It's about looking at things a bit different that we've been "programmed" to do in the aquarium hobby for so long. It's about not being afraid to question the reasons why we do things a certain way in the hobby, and to seek ways to evolve and change practices for the benefits of our fishes. 

It takes time to grasp this stuff. However, as with so many things that we talk about here, it's not's simply an evolution in thinking about how we conceive, set up, and manage our aquariums. 

And the idea of "filtration" is as much about incorporating natural processes into our aquariums as it is about employing some piece of gear, perhaps more so.

Think about that the next time you consider what type of "filter" to employ in your next aquarium.

Stay thoughtful. Stay creative. Stay bold. Stay diligent...

And Stay Wet.


Scott Fellman

Tannin Aquatics 



Scott Fellman
Scott Fellman


1 Response

Ben S
Ben S

January 10, 2024

Hi Scott,

I really enjoyed reading this! I’m also a long-time reefkeeper from the 1990s and 2000s (although I currently do not have any because of life’s busy nature). I’m planning to venture into freshwater aquaria very soon, with my first aquarium as botanical. I’m captivated by the life in this environment, so this article was right up my alley. Most of my time in reefkeeping was spent watching the sandbed fauna and flora, lol.

Like you, I also HATE visible equipment in an aqarium. A sump is a must have for me. End of story. The end. I probably will opt for a black background and black returns to blend in. I’m not sure yet what filtration I’ll have in the sump (leaves and debris will 100% be in the display). It could turn into an undertank display, haha.

I’ll primarily be collecting leaves and wood locally since they are readily available, unless I throw in some others (eg, catappa) for variety.

I’ll have a few questions along the way, if that’s okay?

My first question for you: what do you tend to use (or see used) for substrate, and how deep? I’ve seen most folks using some type of sand (eg, pool filter sand), but have also seen the use of “aqua soil”. Given that a true botanical setting (at least locally here) doesn’t have much underwater vegetation, I’m not sure that the later is really called for. However, I could see where some source of fertilization of the root zone could be useful.

I found out the hard way in the 1990s in reef aquaria that, despite the theoretical benefit of a deep sand bed in denitrification, in practice, it was unsuccessful after a few years due to the accumulation of anoxic zones and the formation of literally aragonite “bricks” owing to the relative lack of turnover by sediment dwellers (versus what occurs in the wild). I’m not sure whether an eventual brick wall of benefit (and sudden downfall) would happen in a FW tank. Worth pondering….

Anyways, enough babbling from me. What are your thoughts and preferences on substrate?

Best regards,
Ben in Texas

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