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Aquarium filter setup – for efficient filtration

aquarium filter setup - filter foam

Aquarium filter setup

Filter setup can seem relatively straight forward, with many filters arriving with pre-installed media. You may also think that as long as each type of media is somewhere in the filter, it will do its job. You would be right. But there are ways to make it far more effective.

I recently purchased a JBL E1902, which is what inspired me to write this article. The E1902 arrived pre-installed with media and was described as plug and play, but as I looked at the images of where the media was located in the filter, I knew I needed to change it all around.

Setting your filter up efficiently not only means that it will do a better job of cleaning your aquarium water, it also means that you will have to clean it less. Good news all round!

In this article, I will talk through each type of media, what it needs to do and where you should locate it in your filter. If you would like to read a little on filter flow first, see our short article on it HERE.


Filter flow

Before you begin organising your media, you will need to know the route that water takes as it flows through your filter.

Some flow through media from the top down, some flow from the bottom up and some have a mix of these.

As an example, the E1902 has water flow into the top of the filter where it enters the top tray first. The water then leaves this tray through the sides where it drops to the bottom of the filter. Then it flows back up through the centre through the remaining trays, where it is then pumped back to the tank.

So, if you don’t know how water flows through your filter, give it a google, or ask us in our forum as this is vital knowledge to get your filter set up as efficiently as possible.


filter flow



Aquarium filter setup – Mechanical Filtration

Mechanical filtration is the means by which your filter removes larger objects, such as fish poop from the water.

Mechanical filtration should occur first in the filter. This means that your filter removes larger debris from the water before it hits your biological media. Your bio media will be less effective if it is covered in fish poo!

Mechanical filtration happens in three stages. The first stage should be a coarse sponge, this will remove the largest chunks from the water as it passes through.

Second should be a medium sponge, which removes smaller debris. Last should be a fine sponge/wool that removes the smallest particles.


As an example, the E1902 has a pre-filter tray which is the first tray that the water enters. This is filled with a coarse sponge to catch large debris as it enters the filter.

The water then flows to the bottom of the filter and is pushed up into the second tray. In here I have another coarse sponge, then a medium-density sponge, then a fine sponge.

This means that as water passes through the first two trays of my filter all the debris is removed, but in stages.


Staging the sponges is important. If you only use a fine sponge then all of the debris is caught straight away, whether it is large or small. This causes your sponge to be clogged much more quickly. That means slower filtration and more maintenance.

Likewise, only using a coarse sponge would mean your water still carries all those medium and smaller bits or detritus that could only have been caught by a finer sponge.

Having this detritus caught over three stages means that it is spread through the filter. This means more effective, efficient filtration, and more time between cleaning.


Mechanical filtration need not be expensive by any means, in many cases, those expensive sponges that are designed to fit your filter won’t do as good a job as some of the cheaper options.

The ideal type of sponge for aquarium filters is the reticulated type. Reticulated sponge offers more surface area due to the uneven shape of the surface. So by using a reticulated sponge with the uneven side facing the flow of water, it will be more effective.

If you are looking for a set of sponges then these are ideal: CLICK HERE! (As an amazon associate I earn from qualifying purchases).

This set of sponges cost (as I write this) £8.20, once cut to the correct size for your filter you will more than likely be left with more than one of each density to use. Bargain!


aquarium filter setup



Aquarium filter setup – Biological media

Biological media is arguably the most important part of your filtration. Your Bio media is what removes toxic ammonia and nitrite and in some cases nitrate, from the water.

Without Bio media, most fish tanks would be wiped out within a matter of days at best. So it is definitely worth investing in the best stuff.

After mechanical filtration has occurred in your filter your water should be pretty free of debris. So now it is time to remove those toxins from the water. So, your next filter tray or two should contain Bio media.


There are many types of Bio media available, most of them will do the job but some will do it a lot better than others. The idea of Bio media is to provide space for bacteria to live and remove those prior mentioned toxins by consuming them.

Some Bio media’ also provide internal space for bacteria to live, rather than just on the surface. This not only provides more surface area but it also allows some anaerobic bacteria to survive which helps to keep nitrates down.

There are millions of Bio medias available to choose from, so I couldn’t possibly talk through them all. Instead, I will tell you my top two which cover all the bases as far as I am concerned.


First up, and the one I am currently using is Seachem Matrix. Seachem Matrix is essentially broken up pumice stone. Pumice stone is quite porous so it does provide some internal area where bacteria can live.

Seachem Matrix is relatively inexpensive and you don’t need too much of it for it to be effective, based on Seachem’s guidelines. 1 litre of Seachem Matrix costs just £16.99 and is enough to filter up to 800 litres of water.

Seachem advises that it lasts forever and can be washed under the tap, due to its vast internal space where bacteria is safe from the tap water. Personally, I wouldn’t risk that though, and I would probably replace it every few years. But at £16.99 that isn’t too much of a problem.


seachem matrix


If you feel that your filter might benefit from adding some Seachem Matrix, you can find it HERE. (As an amazon associate I earn from qualifying purchases).



Next up on the recommendations list is Biohome Ultimate. This stuff is really the best media in my opinion and is only second due to two reasons:

First, it isn’t cheap in comparison to Seachem Matrix and second, you need quite a lot of it to achieve the desired effect.

That isn’t to say that it won’t do its job unless you have a metric tonne of the stuff. But in order to reduce nitrates to the extent that it is designed to. The advised amount is between 1.5 to 2kg per 100 litres of water.

At a price of £47 for 3kg, this isn’t cheap if you have a larger tank, it also means you need a lot of filter space to house it.

Biohome advises that this media will last for 8 – 10 years provided your mechanical filtration is good prior to your water hitting it. This prevents the pores of the material becoming blocked meaning it keeps on working. So if it lasts that long, the value for money would increase a bit.


biohome ultimate


Biohome media really is great stuff, so if you are looking for the best media available and have some cash to spare, you can get hold of some HERE.



Aquarium filter setup – Chemical filtration

Chemical filtration isn’t always necessary in your aquarium filter. in fact, in a healthy aquarium, it isn’t necessary at all. However, if you do want to add some chemical filtration, such as activated carbon, then it can be added anywhere after the mechanical filtration. Personally, I would have it in the last tray that the water passes through.

Chemical filtration is mostly used after medicating an aquarium, or if you have excess nutrients in the water. The same effect can be achieved with water changes though and a good maintenance routine. It does have its uses though and it can help to keep your aquarium clear if needed. But if you follow this little guide, you won’t need it.


If you do feel the need to add some activated carbon then I would recommend All pond solutions, Theirs is pretty cheap and does the job well. You can find it HERE. (As am amazon associate I earn from qualifying purchases).



Aquarium filter setup – Extras

There are a whole host of additional products that can be added to your aquarium filter, but most should be unnecessary if you have a good regular maintenance routine.

There is however one that I swear by, and that is Seachem Purigen.

Seachem purigen is technically a Bio media as it absorbs nitrogenous compounds from the water before they break down into toxic substances such as ammonia.

This means that life for your other bio media is a little easier and it will help to prevent you having any ammonia or nitrite spikes. This is especially useful in a heavily stocked tank.

For a full read up on Seachem Purigen, see our short write up on it HERE.


seachem purigen


I highly recommend this stuff and always have a bag in my filter. If you fancy giving it a try, it is available HERE. (As an amazon associate I earn from qualifying purchases).

Add this last in your filter to keep it working for as long as possible. In a similar way to your bio media, it won’t work as well, or for as long if it is immediately covered in fish poop.



Aquarium filter setup

To sum up, having your filter set up in this way will make your filter far more effective. It will also mean that your media lasts longer and you will have longer between maintenance.

This is based on an external filter, but if you have an internal then the principle is the same, though i appreciate not all internals allow for multiple layers of filtration.

So it is ideal all round.



Given this a try? Let us know what you think in the comments.

Got a better way? Write it up and submit it as an article, we’ll publish it for all to read.



Found this article useful? Check out the rest of our blog page HERE.

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I am a fish keeping enthusiast with over 20 years experience. I currently keep American Cichlids (CA) which are my favourite fish to keep so far. I started Seriously Fishy as I noticed a large volume of people on various web pages looking for help with Aquarium basics. I created the first Seriously Fishy book to solve the issue in 28 pages, that led to the Seriously Fishy UK fish forum and blog.

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