Algae Scrubber Basics

Clog Prevention

Please note: This is the version that was posted online in early 2012.  While the majority of the information presented here is still correct, there are a few things that are outdated.  I've been meaning to update this for quite a long time, if you have any questions, you can click the Discussion tab and ask!

Bud (Turbo)

Slot pipe clog prevention

This issue is brought up on a pretty regular basis.  Obviously, no one wants an overflow pipe to clog and overflow their tank.  Most people take precautions to prevent livestock from entering the overflow pipe, such as an intake screen.  In the case of the scrubber, they’re worried about the algae growing thick enough to stop flow at the point where the screen and pipe slot meet.

Almost without exception, this question is posed by someone who studies the design, but has never actually built or operated a scrubber for any length of time.  I’m not trying to belittle anyone posing the question by saying that, rather just making the point that if you run a properly built scrubber, you’ll understand that this is really not a concern.  Here’s why:

If you properly build and maintain a scrubber, there is virtually no chance that algae will grow thick enough to block the slot.  I’m not saying that algae will not grow at the junction point of the slot and screen, it most certainly will to a certain extent.  The water on the screen below the slot will get partially diverted over the top of the algae mat, as water takes the path of least resistance.  As you approach the slot, the flow area is restricted to the narrow space between the pipe slot and the screen.  This creates an area of flow pressure under which algae cannot grow to any significant thickness without succumbing to the pressure of the flow and releasing from the (smooth) screening material.  Proper cleaning of the slot and the smooth portion of the screen during weekly screen cleanings virtually eliminates any chance of the slot clogging.

As for the interior of the overflow pipe and slot pipe, these can be clogged by variety of means.  The most obvious of example is a snail, anemone, or other tank mate that makes its way down the pipe.  This is a potential problem for any overflow pipe, but adding a slotted pipe with a cap on the end just makes some people nervous, because there’s no place for that obstruction to exit the overflow pipe.  Fortunately, this is only a problem when you insert the screen too far into the slot pipe.  If you only insert the screen far enough that is extends about 1/8” to ¼” above the inside of the pipe, then anything that makes it all the way through the plumbing to the slot pipe will get pushed to the end of the pipe by water pressure, and should only partially block the flow, and only at the end of the screen, if at all.

If you insert the screen all the way into the slot until it contacts the inside of the pipe, the obstruction could form at the beginning of the slot tube, and could substantially or completely block the water flow.  However, this is perfectly fine as long as the inlet to your overflow pipe has a strainer on it that would prevent anything from entering the pipe.

I don't know if there is any advantage to full insertion vs. minimal insertion.  Inserting the screen further into the slot pipe may even the flow out a bit, but I haven't noticed any glaring issues with the way I do it.  This is why I recommend inserting the screen such that it protrudes no further than ¼” into the interior of the slot pipe.

With all that said, if you’re still concerned about the issue, and don’t want to take any chances at all (and you would be hard pressed to find someone to blame you), then there are a few techniques that can be implemented that will reduce or completely eliminate the chance of a blockage of the slot pipe causing your tank to overflow.  Notice that I only mention a blockage of the slot pipe.  This is because a blockage of the overflow plumbing before] the slot pipe is a totally different issue, but some of the solutions below will apply to both.

Screen modification

You can remove some of the horizontal pieces from the smooth section of screen, the idea being that with the horizontal portion removed, there will be a faster flow of water and less area for the algae to attach to.  Something like this:

The larger open space means that cleaning off the algae that grows between the squares is much easier.  I haven’t seen many people use this technique, and haven’t had much feedback either way, but I would expect that this could result in slightly less flow impediment at the junction point, which might mean slightly higher flow requirements in order to get even flow coverage.  But that’s just a guess.


Originally, it was recommended to place crosscuts in the slot tube.  You will see this on older builds.  This is not recommended anymore, so don't do it.  The idea was to allow for water to continue to flow if the algae grew up into the slot and clogged it, and also to prevent squirting.  The result was that algae grew easily into the slot, because the pressure wasn't high enough to prevent it - flow was just diverted to the crosscuts.  Then, the pressure was higher through the crosscuts, which resulted in squirting.  In essence, crosscuts created the problem which they were supposed to solve.  This is basically how the concept of pressure preventing growth (as described above) was brought into focus.

Herbie or BeanAnimal

The best way to run a scrubber, for more than one reason, is to feed directly from the full siphon standpipe of a Herbie (2-pipe) or BeanAnimal (3-pipe) system.  I don’t want to go into a large amount of detail about these systems, or debate the advantages or disadvantages, so I’ll just briefly describe them.

These systems utilize the concept of the “tuned” standpipe; the first standpipe (“Siphon”) has a valve on it that can be adjusted until the rate of flow through that pipe is just below the rate of flow of the return pump, and the second pipe (“Open”) handles the excess without gurgling and flushing.  The BeanAnimal system uses a third “Emergency” standpipe and has a modification to the “Open” standpipe that allows that pipe to “take over” as a full siphon in the case of a total blockage of the “Siphon”.

These systems are designed with a backup standpipe that is able to handle the full flow of the system in the case of a partial or total blockage of the main siphon pipe.  This allows for the full head pressure of a column of water above the scrubber slot, which results in a higher pressure at the slot and even less chance of algae growth near the slot.

There are other considerations when running a scrubber off a tuned pipe system that I don’t want to get into here.  I just wanted bring that option to light.

Slot pipe bypass

On some early designs, you can see a PVC tee in the overflow pipe for an “emergency” or “clog bypass”.  The thought process was similar to the “crosscuts” idea, in that water would flow through the “bypass” if the slot pipe got clogged with algae growth at the pipe/screen junction, and the result was the same.  What would usually occur is that the “bypass” would run very easily and not allow pressure to build up at the pipe/screen junction, and occasionally it would divert flow completely.  This also helped bring “pressure preventing growth” into focus, and thus it is not recommended.

However, there is a modification of this concept that will allow the pressure on the slot pipe to stay high, while still allowing for an “emergency” or “clog bypass”.  The key is that the alternate branch of piping must be as high above the slot pipe as possible, and must not be a closed pipe (or it will siphon).

Here is a sketchup of the basic concept:

The left side represents the overflow pipe that directly feeds the scrubber.  The first PVC tee can really be placed anywhere with any orientation, but lining up the primary flow through the ends is best, with the bypass flow coming out of the side of the tee.  The bypass line should then elbow upwards as high as possible, then elbow over to horizontal into another tee.  The pipe below the second tee extends to the sump.  The pipe above the tee provides an anti-siphon relief and should extend to the top of the trim on the tank.  The bypass pipe should be one size larger than the rest of the plumbing from the point of the second tee to the sump, at least in my opinion.

If the overflow is from a drilled bottom / reef-ready tank, this means that you will have to run the bypass pipe up about 1/2 way up the back or side of the tank, keeping in mind that the level your standpipe/durso inside the overflow in your tank will need to be several inches higher.  If you’re running this of an HOB type overflow, you still want the first tee as low as possible, but since you already have the back of the tank to work with, you can place it before you elbow towards the sump, then go vertically up the tank and elbow over to the second tee.

The important concepts to follow here are 1) the second tee is higher than the first, preventing free-flow through the bypass, 2) the second tee is high enough to prevent unwanted bypass, 3) the bypass line is not allowed to easily form a siphon, and 4) the bypass line should be able to handle 100% flow from the tank in case of a blockage before the slot pipe.

All pipes should be welded (not friction fit) and appropriately supported and secured in place, such as with straps or clamps on the stand or a wall.