How (and why) to Plug the Bypass Opening on Your Fluval Spec Aquarium

I discuss a bit in my Fluval Spec V review about the design of the filtration system in the Spec series of aquariums and, specifically, what that little slot is in the back wall (toward the bottom). I’m going to try and explain why it is there, help others decide if they need it, and offer instruction on how to modify your Spec to close this bypass if you want.

The Spec Auxiliary Flow Slots – Purpose:

lower bypass opening in fluval spec aquarium

There are two auxiliary flow slots in the Fluval Spec line of aquariums.  The first is about half way down the dividing plastic piece that separates the display section from the filter section.  It is about 1″ long and the same width as the slots at the overflow up top.  The purpose of this bypass seems straightforward: if the water level in the aquarium gets too low (from evaporation over time) the water would no longer overflow into the filter section and the pump would then run dry.  By adding this little slot at the bottom, Fluval ensures that even if a user allows the water level to get below the bottom of the overflow slots up top, water will still flow into this little secondary slot and the filtration system will still operate.

bypass opening in baffle between pump and filter sections of fluval spec aquarium

The second bypass is near the top in the dividing plastic that separates filter section from pump section.  It is horizontal and is right at the top of the stock filter media block. It’s a little less clear what this bypass does but I believe it’s still related to keeping the pump supplied with water.  If the filter media was to become very clogged with debris, this slot would allow water to bypass the filter block entirely and flow into the pump section.

Reasons to Plug the Filter Bypass:

While the two bypass slots do add a level of safety to keep the pump supplied with water, I don’t feel that they add to the performance of the aquarium for how I will use it.  If you are willing to keep the water level above the bottom of the overflow slots and are willing to keep the filter block reasonably clean, they serve no positive purpose.

The two bypass slots will allow water to flow around the filter media, which is not what I want.  I want all the flow to be forced through the filter media to help clean debris from the water.

How to Plug the Bypass Slots:

The best way to close the bypass slots is to use aquarium safe silicone sealant.  The reason you want to spend a bit more for ‘aquarium safe’ is because plain silicone sealant you get at the hardware store may have anti-fungal chemicals that are toxic to your fish and inverts.  There are several brands to choose from; I bought aquarium safe silicone from Marineland and it worked very well.

The picture at the top of this page shows the lower slot closed off with silicone.  It’s simple to do, just put a nice bead in the slot and smooth the display side with a wet finger if you wish to make it look more finished.  Leave it to dry for around 24 hours.

I have also heard of people using a bit of foam or other material shoved in the slot to close it off.  This could be a good solution for those who already have a working aquarium filled with water.  The disadvantage is that the material would be more visible and may not completely close off water flow.

Waiting Till Later to Plug the Bypass Slots:

You may be tempted to get your aquarium up and running and then decide if you want to close off the bypass slots later.  I’d encourage you to go ahead and fill them in with silicone sealant now rather than later.  It’s extremely easy to do this with a brand new tank before it is filled.  After it is running, you have to have the area very dry and it has to remain dry for a day after you apply the silicone.  This will be very hard to do in a working aquarium with inhabitants.

If you decide later you don’t want the slots filled in, it would be very easy to remove the silicone with a sharp object and pick the pieces of silicone sealant out.

Alternatives to Using Silicone to Block the Fluval Bypass:

Since I wrote this, InTank Aquatics has come up with a product for purchase to plug the bypass in the Spec V and Spec Evo.

I have had several commenters below give creative ideas for plugging this opening.  The most interesting was from ‘Louis’ who discovered these USB Dust Covers (who knew such a thing was even needed?) that fit in the opening.  I haven’t tried it, but that sounds like a good workaround if the tank is already operating.

38 thoughts on “How (and why) to Plug the Bypass Opening on Your Fluval Spec Aquarium

  1. I just got my hands on a spec V and at the moment I’ve got a heater and my substrate on top of everything that came with the tank. I was wondering if it would be okay to fill with tap water and the conditioner to get the cycle going while I wait to get my decorations and plants.

    1. Yes, you can get it all set up and filled with water and let it run prior to getting the plants in. I’m hoping you understand how to start the cycle; I used drops of pure ammonia to feed the start of the beneficial bacteria. I really do need to write a page on starting a fishless cycle. Good luck!

  2. Hi Nate, thanks for all of your very informative articles! I just came across this one after setting up my spec 3 (unfortunately, otherwise I would have used your silicone method!). It’s been running now 4 days w/water, driftwood, plants & an arsenal snail that hitched a ride w/the java moss. I haven’t put my betta in it yet because I’m waiting on the master test kit I ordered to test first. In any case I’d like to do what you did by closing off the slots & am not sure the best way to achieve this since it’s up & running. Any suggestions? You mentioned foam stuffed into the slot, is there anything better & the best way to do it? Also, when you first set up either of your specs did you notice an oily residue floating on top of the water? Do you know what would cause this (especially since it’s fish less & am only feeding the tiny snail a very small amount of food)? Any suggestions to get rid of the oil deposits?
    Thanks in advance for your time!

    1. If you don’t have a fish yet, you could manage to fill with silicone. You could drain the tank down below the bypass (this is pretty low, however); get everything dry around the bypass opening, fill bypass with silicone, wait for it to cure, and fill. The cure time is something like 24 hours, but I think you might be able to cheat this down to around 16-20 hours. This will not be easy, which is why I suggest doing it before the initial build.

      After the fact, I still think covering or blocking with something would be best. Foam is all I can think of at the moment. Let us know what you come up with.

  3. Has anyone with a 3D printer just made a “plug”, think flat front that covers the hole, with a tab coming off at a 90degree angle (think T) that inserts into the hole to keep the front part in place. Should be super easy to make, if you have a printer, heck I would buy one. That way people like me that didn’t read your post before they got their tank up and running could easily cover this hole (the front one is what I am having the problem with). Just a thought…

    1. yeah – super easy. For someone with a 3-d printer, modeling and design experience. But you are right, that would be nifty for sure!

  4. what benefits does plugging the lower intake provide other than prevent fin damage? how does it effect the flow in the tank? does it make the filtration work better?

    1. Yes, it improves performance of the filtration system by forcing the path of water through the filter media (as opposed to bypassing part of it).

  5. Easy solution to the bypass plug on a full tank! Search Ebay for a USB silicone port plug. Cut it in half lengthwise with an exacto knife along the top edge and squish it into the bypass. It is a perfect fit. I had only a clear plug, but you can order an entire bundle of them in black for about $0.74

    1. Thanks Tiffany will follow your idea. Appreciate you sharing this.

    2. I love this idea!
      Question: Nate, I noticed you mentioned something about how some silicone sealant is not safe for aquarium use. Do we know if the silicone material used to make this USB plug is safe for the fish?

      1. No idea. Someone who has tried it would have to chime in.

    3. Wow so many great suggestions. I am slightly overwhelmed as I am just helping a friend set up his new Fluval Spec V. But non the less… I cut a small piece of the filter suction cup ring (which you don’t need and can’t fit anyway)- and wedged it into the lower intake slot. Perfect fit. We’ll see if it works. Setting up the tank later today. QUESTION? Since my heater (Tetra ) is in the chamber with the tube – I am assuming I need a few holes in the output tube? I am also ready to go with some suggested options to reduce flow. So back to the QUESTION? Should I have the filter pump on High, Medium or Low or is that something I will be able to discover after I get the water in the tank? The aquarium will have 1 Betta and 2 Guppies moving from a 3gal. Very exciting!

  6. Can anyone actually see water bubbles, debris being sucked in from the top of the aquarium and into the filter?

    I’ve got the lower bypass hole plugged off (I tested it by removed water from the tank below the top vents and running the pumped water into a bucket. The pump and filter section ran dry), the pump is on full power but bubbles, debris and fish food float right on by the top overflow vents and never go into the filter.

    I assume water is being sucked in somehow, but I’m unsure how effective it is.

    Any thoughts?

    1. When I stir up debris during my weekly cleaning, I can clearly see particles in the water being drawn through the overflow and into the filter system.

      1. Thanks for the reply Nate.

        I watched for this when I cleaned my tank on the weekend. You are right, there are small particles being drawn into the overflow vents and into the filter. This seems to be happening below the top surface. On my tank, bubbles and oily film on the surface don’t seem to be pulled into the vents, but particles below the surface are being sucked in.

  7. I will be getting the Spec III and putting a Betta in the tank. Should I seal up both bypass slots or just the one in the display section?

    1. I’d do both to start out. If you decide that you don’t need the divider one plugged, it will be very easy to cut it out with a razor after the fact.

  8. One thing to keep in mind, if you plan on using hot glue or silicone, is how to remove it.

    We recently went on vacation for 2 weeks and I was concerned there would be enough evaporation of water that it would drop below the upper flow vents.

    I have been using a silicone usb plug that I purchased on Ebay (thanks to the poster above that suggested it) that seals the vent perfectly. Before I went on vacation, I simply removed the plug.

    If it were silicone or hot glue, it may not have been as easy to do

    1. Thank you for your advice! As long as hot glue will be safe for my fish I will be satisfied.

  9. If the tank is already up an running, you can use reef safe epoxy (for mounting corals) to plug the hole up. I did this when I had it as a pico reef. I forgot to plug it up when I converted it to a betta tank (I removed the epoxy when cleaning and disinfecting for the switch), so now I am getting ready to the same thing. seemed to work as well as silicone would have. It will be visibal, but it works.

  10. The filteation system in that Fluval tank is a terrible design. It takes so much space and dows very little. My son hates it and says it sucks. I think having the input of the pump on the opposite side of the foam section is nor helping.

  11. Found this for plugging the lower return opening on the Spec 3 and 5. $1.99 each. You can install even after you have water in the tank, just push it in.

    Works on the Fluval Evo 5 as well.


    1. That’s a pretty good option for a tank that is already started.

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