The filter you use...The filter you have.

When it comes to keeping botanical-method aquariums, I realize that we spend a huge amount of time talking about mindset, mental shifts, preparation, ecology, etc., but scant little time talking about less exciting, more "nuts-and-bolts" stuff, like...filtration.

So let's tackle that today! Now, it's not the first time that we've covered this topic over the years here, but it comes up a lot, so it's worth discussing again.

First of all, what do we mean when we talk about "filtration?" To me, filtration can mean a mechanical, chemical, or biological means to remove unwanted "stuff" from the aquarium water. (Do you like that "stuff" part? VERY scientific, huh?ūüėā)


In a botanical-method natural aquarium, filtration and its companion, 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.

Are they a "burden", though?

These items not only are part of the "hardscape"- their very 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 physically breaking down, releasing not only "bits and pieces", but dissolved organic materials as well. 

That's where filtration comes in.

Now, Nature provides "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 meandering, yes. We'll get back to that. 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.

Now, as fish geeks, we aren't just going to rely solely on bacteria and fungi to do the "heavy lifting" of filtration for our tanks...I mean, we could, in theory. However, in practice, we need some help. That's where "filters" come in. The first consideration is, of course, choosing a filter system of the appropriate size for the tank you're working with. That is kind of a "no brainer", since we typically all know how to do that (ahhh, I'm assuming)- and if we don't, we can easily research this topic on hundreds of sites all over the 'net. 

The other consideration is what you're trying to achieve with a filter system. Is your goal to remove bits of particulate matter from the water column? To chemically adsorb/absorb nutrients or unwanted compounds? Or, is it to facilitate the growth of beneficial bacteria and encourage biological assimilation of organics? Ohh, we'll come back to the last one later, okay?

Let's "cut to the chase" here:

At the end of the day, you can use pretty much ANY type of aquarium filter in your botanical-method aquarium: Cannister filters, inside filters, hang-on-the-back power filters, sponge filters, "matten filters", sump systems, all-in-one aquariums...Hell, even under gravel filters if you're old school! It really doesn't matter. They can all get the "job done"- assuming that the job is to accomplish one of the things I just mentioned.

I think that the "big issue" which forms the basis of a lot of the inquiries we receive from our community about this topic is what kind of filter media you need. This comes up a lot because many hobbyists relish the tinted water, and are rightfully concerned about whether or not popular chemical filtration media like carbon will remove the tint we all love.

Activated carbon.

Personally, I love the stuff, and rarely, if ever have ran an aquarium without it.

My bias towards using carbon in my aquariums comes from years of keeping reef aquariums, and later, co-owning a commercial coral importation/propagation facility, which had thousands and thousand of corals in tens of thousands of gallons of water.

Corals produce copious amounts of slime, mucous, and metabolic waste, not to mention "allopathic compounds" (ie; chemical "weaponry" used to defend their turf against intruders), and carbon, along with admittedly more efficient means, such as ozone and protein skimming, formed a sort of defensive "triad" to keep the animals healthy and water quality high.

Oh, and we also employed water exchanges, of course.

And yeah, we used a "shit ton" of the stuff in our facility! 

For reefers, the benefits of carbon use are really pretty apparent:

It reduces discolorations in the water.

It may bind some organic toxins.

It can be a place for beneficial bacteria to use as a "culture media."

It may remove copper and other trace metals (which bind to organic matter which, in turn binds to activated carbon for removal.

What about for us- the botanical-method aquarium crowd?

As we've discussed many times here, there is a sort of obsession those in our world have about keeping the water in our tanks dark and earthy-looking, and the idea of using chemical media with known adsorbent capability like carbon seems a bit "counter intuitive" to some. Carbon does excel at removal of compounds like phenols and tannins.

I'll often tell people that I use it more-or-less "full time" in my blackwater, botanical method displays, and this elicits the online equivalent of raised eyebrows now and again. "Tinters" will ask, incredulously, "Doesn't this stuff remove the color from the water?"

To which I respond, "Yes, it some extent."

Please DO look at some pics of my tanks, and tell me if I've been removing "too much" tint via my use of carbon!

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.

(Activated carbon "pro tip":  Since It will remove the colors imparted by tannins, if you use the amounts most manufacturers recommend, just use less. Like 1/2 or 1/3 the recommended amount. Or, consider the use of other less "indiscriminate" chemical filtration media.

There are a lot of different chemical filtration media out there, and not all of them will remove the color imparted by tannins. "Now, the tough love" part?  I can't stay up on all of them, largely because I don't use them. It's not my job to direct you to the right one, okay? It's yours. Do your homework. You can do it!)

It should be noted that activated carbon does not remove all possible toxins or unwanted chemicals, including the ammonia produced by animals, and nor does it substantially affect carbonate hardness of the water. Other compounds that activated carbon has little or no ability to remove include stuff like calcium, carbon dioxide, fluoride, magnesium, nitrate, nitrite, phosphates, sodium, and iron.

Of course, it's important to use carbon correctly. Ideally, carbon should be placed after the mechanical filtration media in the filter, where water will flow through it with little restriction. Otherwise, the stuff will clog with debris and other solids, significantly reducing its available surface area for chemical adsorption. Make sense?

Oh, and in these scenarios, activated carbon does recruit biofilms and their constituent bacteria, becoming a sort of biological filter. So, although this could be seen as a sort of collateral benefit, if you let your carbon sit too long, in a strange twist of irony, the sudden removal of portions of the natural biological filtration could actually be counter-productive-cause a sudden decrease in water quality!

The reality, in my opinion, is that even carbon is not really a full-on "necessity", if you're on top of other aspects of husbandry, like water exchanges, etc. 

And what about filters in general?

When you break it down, a "filter" accomplishes the things which we discussed previously- Physical removal of materials from the water column, chemical adsorption/absorbtion, facilitates biological activity (ie, the growth of beneficial bacteria), and circulates and/or aerates the water.

Think about this: If we consider the functions that a filter unit/system does, it's not much of a stretch to conclude that a botanical method aquarium, replete with all of these leaves, seed pods, and such, functions in a way as the "filter."

Shiiiit. Woahhh! ūüí•


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

Think about this:

The botanical materials present in our systems provide enormous surface area upon which beneficial bacterial biofilms and fungal growths can colonize. In addition to physically fragmenting botanical materials, 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 hauntingly 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 articles and videos 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. They are perfectly natural. We may not see the famous long, stringy "snot" of our nightmares, but the reality is that they're present in our tanks regardless.

Attempting to remove them because they look "weird" to us is just...well...stupid!

And wasteful.

The 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 ( by our own hobby definition, a "filter" of sorts?), they also represent a beneficial food source for fishes. They are shockingly useful.

Now, look, I can see rare scenarios where disproportionately 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. I have seen/heard of this happening literally 3-4 times in over 7 years of running Tannin Aquatics, and every single one was attributable to the misstep I just mentioned.

Typically, however, biofilms are far more beneficial than 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! (extra credit "homework": Research "bioballs")

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-method 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.

Chew on that for a few minutes...

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.).

And never forget our friends, the fungi!

Okay, great. I've just talked about decomposing leaves , biofilms, and fungal growths 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) Utilize a "filtration system" which you like, if any.

"So, what filter do you use, Scott?"

Personally, I use a lot of "all-in-one" tanks, which have a built in "filter compartment" in the back, which one could (if he/she/they desires) add chemical filtration media. I generally use...nothing in mine. Okay, well, maybe a small sachet of carbon.

But that's it. 

Again, I feel that it's far, far more important to facilitate biological processes in our tanks than to develop a sort of "dependency" on mechanical and chemical filtration systems. Learning to manage our systems naturally with water exchanges and careful stocking/feeding is far more important, IMHO.

Oh, and decent water movement/circulation and gas exchange. 

If you do your homework about some of the natural aquatic habitats which inspire our work, you'll find that the majority-not all, of course- have some water movement. They're usually not stagnant (although some are).

In an aquarium, we're well-advised to have some water movement, to facilitate gas exchange, provide a little "exercise" for our fishes (that sounded stupidly quaint, but you get the picture), and to avoid thermal, pH and/or nutrient layers in our tanks.

Gas exchange (the process in which carbon dioxide exits into the atmosphere and new oxygen from the atmosphere is dissolved into the water) is really important in aquariums, and aeration from filter returns helps facilitate the process. Fish need oxygen (like 5-6 parts per million) in their water. Now, it's not mandatory to have airstones, filter returns, or surface skimmers to create surface agitation, but it sure helps.

I suppose you could say that the "purpose" of aeration is to "break up" the surface of your water. You’re not going to separate the oxygen molecules from the water and force a gas exchange within the water column, by cranking up an ayirstone- that's not what it does. But it will help break up the surface boundary layer to facilitate gas exchange. I guess that's why I love surface skimmers, or filters which skim the surface boundary layer.

And yes, a wide aquarium with lots of open surface area can accomplish gas exchange without supplemental circulation, too. Not as efficiently as mechanical means, but it works. I mean, hobbyists did this for a generation before air pumps and filters came along, so...


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. It's no longer a "cookie cutter" recipe for success in the aquarium world; it's okay to experiment a little.

Just understanding that the aquarium is an ecosystem unto itself will help you make more informed, less restrictive decisions about what works best for you and your tank.

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. Of course, there are lots of different viewpoints on this topic!

Like so many things that we do in our hobby speciality, considering filtration and its place in our work requires that we look at things from a variety of angles. It's never just a "cut-and-dry" recipe for doing things a certain way; everything requires a little more consideration, doesn't it?

It does.

Stay focused. Stay thoughtful. Stay curious. Stay proactive...

And always Stay Wet.


Scott Fellman

Tannin Aquatics 



Scott Fellman
Scott Fellman


2 Responses

Mian Hasnat
Mian Hasnat

April 02, 2024

Your article about aquarium filtration is really helpful and a valuable resource for anyone looking to maintain a healthy aquatic environment. You can explore the best filters for your fish tank by

Mian Hasnat
Mian Hasnat

April 02, 2024

Your article about aquarium filtration is really helpful and a valuable resource for anyone looking to maintain a healthy aquatic environment. You can explore the best filters for your fish tank by Clicking here

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