Protein Skimming: What, Why and When

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I thought the forum would like to read something I wrote:

Protein Skimmers have been around for at least the last 60 years and have come in a wide variety of forms and efficiencies. The first protein skimmers were simple triangle pieces of glass that were fit into the side of an aquarium, and powered from the bottom up with a simple wooden air stone. Inside of the unit, there would collect on the glass a very slimy, brown and green sludge which would then be cleaned off manually (Goldstein 46).

Protein skimmers are also known as foam fractionaters. The purpose of a protein skimmer is to remove organic waste from the system before it has a chance to break down into ammonia. An efficient skimmer can remove up to 80% of the organic waste products that are produced in a closed system (Hunt 46). You can think about the bubbles in a protein skimmer like the bubbles from soap when you wash your hands. The bubbles act as a surfactant, gathering and denaturing proteins and other organic molecules. Denaturing proteins is quite common – adding heat to eggs makes the egg cook, but, the proteins can also be denatured by the use of vinegar or lime juice. The acids make the proteins unfold, which causes a change in its chemical structure. The process of violently injecting oxygen into saltwater denatures these proteins. In turn, the proteins become very, very sticky and pick up other, larger molecules and particles in the water column (Goldstein 47). The longer the contact time that the bubbles have with the water, the more debris the sticky proteins can pick up and deposit in the cup (Goldstein 47).

The benefits of having a protein skimmer is enormous. It removes this built up organic waste, which would otherwise be washed away from a reef in the ocean and broken down by deep sand beds later. Since we have closed systems, a protein skimmer is a great way to increase the long term success of any saltwater aquarium. By removing 80% of the potential waste from the system, and leaving about 20% of the waste in the system for the corals and macrofauna to eat, you are ensuring that everything in the system gets fed, and there isn’t an excess of nitrogen and phosphorus in the water column that could cause problems with nuisance algaes, dinoflagellates, and cyanobacteria. By using a protein skimmer, you are removing organic materials before it has a chance to break down into ammonia and nitrogenous waste which can weaken livestock (Brightwell 46).

There is some debate whether to skim or not to skim among hobbyists. In addition to removing organic wastes from the system, they have been shown to remove trace elements, including saltwater from the system. The other issues are that because the organic molecules are so sticky – they also remove food from the system that could have been eaten by fish, corals, and other desirable invertebrates. Other organisms are also removed by protein skimming, including beneficial bacteria, microscopic plankton (algae), small crustaceans and other zooplankton (Hunt 48). It is of my opinion that protein skimmers definitely have their place in reef aquariums large and small – and many aquariums do benefit from the addition of a protein skimmer. There are some systems – like fish only systems and some soft coral systems that shouldn’t need a protein skimmer, but rather regular water changes.

There are many factors which can affect the efficiency of a protein skimmer. The air flowing into the skimmer, the water being pushed through the skimmer, the bubble contact time, the aquariums temperature, salinity, pH, surface tension and types of compounds removed all play a key role in the efficiency of a protein skimmer (Delbeek 120). Manufacturers tend to run tests under completely ideal conditions and label their products accordingly – therefore a skimmer that is manufacture rated for a 100g tank may only skim a heavily stocked 65-75g aquarium. It is always a good idea to go “Plus One” when choosing a skimmer – which means take into consideration your size aquarium and then choose a skimmer that is rated for an aquarium one step up from yours.

The amount of air and water flowing into the skimmer determines how large the bubbles are and how much contact time they have with the organic compounds in the water. If the bubble size becomes too small and start to reach a supersaturation surface tension point, the bubbles will actually form larger bubbles which have less ability to hold organic waste, and the “foam head” at the top of the collection collar will collapse (Delbeek 120).

The typical pH of a reef tank will vary over the course of a day, but it will have an effect on how efficient the skimmer is. At the peak of the day, when the pH is the highest, your skimmer will foam the most – since the electrostatic attractions and affinity of organic molecules to the bubbles will increase. To make your skimmer more efficient, you should try to keep your pH between 8.0 and 8.3. The more stability that the pH has, because of a stable alkalinity (~10dKH), the longer the foam head will stay and the more particulate matter will form (Delbeek 122).

Temperature affects the efficiency of protein skimmers because as the temperature increases, the surface tension decreases. In water that ranges between 80*F to 90*F, you don’t expect a skimmer to be able to produce small enough bubbles for it to create a nice foam head. By keeping your aquariums temperature stable and below 80*F, you are ensuring that your skimmer is producing consistent results. However, the effects of temperature on dissolved organic matter can vary – because at a higher temperature you may be getting a different type of organic compound being skimmed out than if you were at a lower temperature (Delbeek 122).

Salinity has an effect on skimming because a higher salinity such a 1.026 means that there is more surface tension, which increases the amount of bubbles that are able to be produced. A lower salinity, such as in a fish only system of 1.20 has a lower surface tension and therefore the skimmer may not produce “ideal” results. However, the results of different salinities and skimmer efficiencies are dependent upon all else being equal (Delbeek 122).

There are many different types and brands of skimmers. There are hang on back skimmers that are great for aquariums that are not drilled. There are in-sump skimmers for those aquariums that are drilled and want a space saving setup. There are also skimmers that are recirculating and external – which means that you can pipe water to them and the pumps there will draw in air and water and send it back to the aquarium. Picking the best skimmer for your tank can be a very daunting task because of all of the options. Here are a few things to keep in mind when buying a skimmer:

If your aquarium does not have a sump and you do not have a lot of room or a separate room, consider going with a simple hang on the back design that has a low profile. If your aquarium has a sump, consider the size of the sump and if you can fit a skimmer into the sump. Pick a skimmer footprint that can fit down inside the sump. If your sump is too small, but you still have room for a skimmer underneath the stand, consider an external recirculating skimmer. The next thing to consider are brand names. Because this article will be outdated before it’s even published (in the world of skimmers), I suggest asking forum members about what brands of skimmers they like and trust. Usually, if a skimmer will function correctly, is easy to install and maintain, it’s a great skimmer – regardless of the price.

DIY skimmers used to be very popular in the hobby. Anything from a 20oz water bottle for a nano tank to a 5g mountain spring water bottle – and even Tupperware. Many aquarists decided to experiment with protein skimmer bodies on their own, and some of them even produced great results. Today, experimentation has led to many different styles of skimmer bodies. One of my personal favorites is a cone style in-sump direct pump fed skimmer. To me, these types of skimmers that have the pump directly inside the skimmer body are not only space savers, but also produce some of the best results. However, that can be argued about by nearly every other owner who owns a different style of skimmer. The most popular skimmers these days are needle wheel base (NWB) skimmers that draw in water and air into the needle wheel propeller to be “chopped up” into smaller bubbles – and pushed into the body of the skimmer.

Adding a protein skimmer to your aquarium is a decision most of us will make in this hobby. Many people will tell you that a skimmer is an absolute necessity. Others insist that it is not necessary at all. What you need to do is make up your mind and figure out if it is just one of the many “tools” that you will find useful to make your aquarium successful. It is not clear when you need to add a skimmer to your aquarium – if at all. Some people start their aquariums out with a skimmer from day one. Others wait six months or more before they decide to buy and install one. Other people opt for other pieces of equipment such as chemical and biological filtration systems which can also decrease nitrogenous waste. The problem is finding out if it is appropriate for you to go ahead and buy one. I personally do not feel like a skimmer is a necessity from day one. I think that an aquarium should start to establish itself over time without a skimmer and a skimmer be added six months to a year later down the line if water parameters are testing above range for that particular system. Utilizing a protein skimmer and cleaning it is perhaps one of the easiest methods of reducing organic matter in the water column, and therefore I believe nearly every system can benefit from it.

Troubleshooting a protein skimmer is rather easy. After your initial installation, it should take anywhere from 2 hours to one week to “break in” during this break in period, organic materials and oils are either being stripped or collected from the unit. You will know that your protein skimmer has broken in after it forms a foam head and starts collecting a thick, dark waste in the collection cup. If your protein skimmer is not removing dark skimmate, you may have your water level set too high and are just removing a very wet skimmate, which may resemble green tea. Try adjusting the skimmers water level down so that it froths. Making small adjustments down very slowly and allowing either a few hours or a day to catch up. Doing smaller changes and “tweaking” the skimmer is much better than large changes over a short period of time – you will never know what actually worked. Always keep your pump(s) free and clear of any large particulate debris such as large rocks, algae, and other things that may accidently enter into the pumps propeller and bind it. If your pump isn’t pushing water up and foaming into the main body of the skimmer, your pumps impeller may have been damaged. Take it out and check, clean it thoroughly – you may even submerge it overnight in vinegar to clean off any calcium/magnesium deposits. Your skimmers cup should be emptied once or twice a week. If your collection cup is very large, you might have to empty it less frequently. If the collar of the collection cup is frequently soiled with organic matter that is not exactly making it into the collection cup, try increasing the water level to try to get more organic matter inside the cup instead of on the collection cup collar.

In conclusion, protein skimmers are a very helpful tool when maintaining high water quality. A skimmer is a way to remove dissolved organic compounds before they break down into nitrogenous waste. A skimmer can effectively keep the pH high by removing excessive amounts of nitrogenous waste. Protein skimmer brands and styles are many – so the best way to choose a protein skimmer is by asking around on the forum what other people have bought and used. Picking a style of skimmer is as easy as knowing what equipment you already have. Knowing how to troubleshoot your skimmer will give you a great idea for the overall health of your system – If it is skimming too much, then there is excess foods/waste - and too little then you may be not feeding enough. Skimmers definitely have their place, and they are just another tool that is used by many aquarists – however, they are not the be-all end-all of filtration. There are many other ways to reduce and recycle Nitrogenous waste besides the use of a protein skimmer.


Brightwell, Chris. The Nano-Reef Handbook the Ultimate Guide to Reef Systems Under 15 Gallons. Neptune City: TFH Publications, 2011. 46-47. Print.
Delbeek, J. Charles, and Julian Sprung. The Reef Aquarium: A Comprehensive Guide to the Identification and Care of Tropical Marine Invertebrates. Vol. 1. Coconut Grove, Fla.: Ricordea Pub., 1994. 116-131. Print.
Goldstein, Robert J., and Michele Bridges. "Protein Skimmers." Marine Reef Aquarium Handbook. 2nd ed. Hauppauge, N.Y.: Barron's, 2008. 46-50. Print.
Hunt, Philip Dale. "Protein Skimming." The Marine Reef Aquarium. Hauppauge, N.Y.: Barrons Educational Series, 2008. 46-49. Print.


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I hate that it didn't break up all the lines from my word document. There should be indented paragraphs etc. Oh well, I guess eventually I'll fix it - if no one else does.
AH! The perfect person to ask! My Protein Skimmer (Eshoppes PSK-200) had broken in, and was doing great. When removing the collection cup the foam would always be right at the top, just short of spilling over. But for the last week and a half, the water level has been going crazy (I'll include a picture). As an example, last night at 9 p.m. I checked and the level was just a bit too high so I adjusted it. I checked at 10 and it was still where it should be. At 10:30 still the same and pulling skimmate (yes, I've actually had to check it this often!).

I got up at 5 a.m. and checked it, still pulling skimmate like a champ and perfectly dialed in. 9 a.m., still the same. 10 a.m. still running great. Then, as has happened all to often over the past week, at 10:30 a.m. the water level dropped over 5". This time, rather than re-adjust it, I let it sit to see if it would go back to where it was. btw, water level in the sump remained constant this whole time. I checked two hours later and the level was still low, and skimmate was accumulating inside the skimmer since it wasn't being pushed up. I relented and adjusted the water level. What I'm expecting is what has happened whenever I readjust these past 10 days. The level will suddenly rise and water will pour out of the collection cup.

All water quality measurements are excellent. I did have a blue face angel with fungus on his gills and was stupidly talked into dosing the tank with Red Reef Rally (BIG mistake). But that stuff should have run its course by now. However, that's when the problem first started.

Other than that, any ideas? See attached photo for what the skimmer looked like at 10:30 this morning when the level went down.


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Yes, no, no, not since it started acting weird, and constantly until I realized the fluctuation in water level in the skimmer affected the sump level.

Mind you my routine hasn't changed in all the time the tank has been up. The only thing was that crap Red Reef Rally but even then it didn't start until days after I stopped using it.

One other thing, on some occasions the water level would be as low as in the picture, but foam would reach all the way into the cup and overflow!
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Well-Known Member
The oils from your hands can cause it to lose its foam head. So can feeding your tank an oily type of food. Different foods will effect it differently.

Having a high increase in skimming might be caused by an excessive amount of organic matter that was released into the water column.

Your skimmer won't consistently skim 100% of the time. Limiting what may cause it to overflow though is important.
Thanks for the response but I don't think you're getting my problem. It's not that it sometimes skims a lot and sometimes a little, it's the wild fluctuation in the water level. It's 6:45 a.m. as I type this. Last night before I went to bed I checked and the water level was just a bit high, the tiny bubbles at the top of the water level about a quarter inch into the collection cup. I adjusted it. This morning the water level was back down to where it was in the picture I attached previously, only today was one of those instances that it was still pushing foam all the way to the collection cup. It must have just started as it wasn't overflowing the cup. I cleaned the skimmate and readjusted again. I will check at 9 or so and see where it's at.

Again, it's not a problem of skimming or not producing a thick enough foam, it's the wildly fluctuating water level (Up to 5" difference). Skimmer is only 3 months old, so it's not a clogged impeller or anything like that. Note that unlike most people I like my house cold overnight. It will get down to about 58. Daytime high around 67. Could that have an effect?

Also, and this just occurred to me, but since my mushroom collection is growing I've started adding Fusion 1 and 2 to my tank. I'm sure you know what that stuff is for. Could that be a cause?
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There are too many variables to say for certain what might be the issue. As long as it consistently skims and you can empty the cup once or twice a week- it's doing its job.


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Is it light green or dark green skimmate? If it's just clear then your skimming way too wet and need to a adjust it down.

If it's dark green/brown or even a lighter green color that often, your tank has too much organic buildup and you might consider a few water changes and blowing the detritus out of your rocks
It's dark green but not a lot of solids. Again, it's not the skimmer's ability to remove skimmate that's my problem, it's the fact that the water level lowers and raises by up to 5" even after hours of working properly.


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The issue then is too many organics in the water column. 3-4 cups a day of dark green skimmate will cause any protein skimmer to be unstable. I wouldn't worry about the exact water level of the skimmer, as long as it is skimming consistently. Once the tank has less organic waste in the system, things should stabilize.

I would think that if your skimmer is building up a decent foam head and starts to skim well, the water line will be either very blurred or nonexistent. My reef octopus Diablo cone skimmer had no water line because of the amount of bubbles it produced. To really give much more advice, I'd have to have a video of before and after. Also, if getting skimmate in the cup isn't an issue, I see no problem at all that needs to be solved.

The skimmer shouldn't filter out large solids- that's the job of a mechanical filter.
No, I'm not getting 3-4 cups a day of skimmate, I'm getting enough that I am emptying the cup just in case the water level rises and washes it all back into the skimmer. There's less than 1/4" of liquid in the cup when I'm emptying it. In fact I rarely get 1/2" of liquid in the cup before the water level lowers and it's no longer lifting anything into the cup.

I wouldn't worry about the exact water level either, if it wasn't dropping over 5" at a time, rendering the skimmer useless, or raising so high as to fill the cup with water which then overflows back into the sump.

I am getting a nice foam. Just below the foam is a section of very tiny but distinct bubbles. That is my water line. Below that is the thick foggy looking stuff that makes up the rest of the skimmer. When I see the distinct tiny bubbles raise up into the cup I know it won't be long before it's overflowing. If I'm lucky I catch it in time. The other alternative is that section of distinct bubbles 5" below the top of the skimmer, accomplishing nothing because it can't push the foam high enough (again, look at the attached picture. You really don't need video to see what I'm talking about).

Finally as for large solids, I meant those globs that are a bit thicker than the liquid but not actually like uneaten food or anything.


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I've been reading this thread and thought maybe I could shed some light.
I think your skimmer is suffering from "Mothers First Baby" syndrome.

When a mother has her first baby (It's a boy!), she worries about whether he's getting enough or the right food to eat. If he gets a skinned knee. If his temperature goes up one degree, she rushes him to the hospital. If his poop is the right color. By the time the second kid comes along all bets are off and she just tosses him/her a bandaid. lol

I think it's the same case here. You worried too much about the white foam and in trying to re-adjust the skimmer, you threw it out of wake and now you can't find the sweet spot again. Yours is a different brand of skimmer than mine but the design is basically the same. As long as the white foam doesn't over flow into the cup your fine. Just keep the white foam about an inch below the over flowing point. It's trying to do it's job but there's really nothing to collect...... yet. Hence the rise and fall of the water/foam level. When it has something to collect, the level will rise above the over flow point and it'll deposit the gunk into the cup. Once whatever skimmate it collects is in the cup the level will drop and the process starts over. Rise and fall. Rise and fall.

Try this: Adjust it down till you JUST start getting micro bubbles escaping from the bottom of the skimmer or there's no foam. Then raise it back up a quarter turn or until the micro bubbles just stop or the foam just starts. Then wait. The next day, do another quarter turn and wait again watching for the rise and fall of the white foam to start. In a couple/few days you'll slowly get it adjusted so that the white foam is at it's highest level needed when it rises, about an inch below the top of the neck leading into the cup. Then just keep an eye on it for a few days to make sure you hit the sweet spot and didn't over adjust it. When it collects enough skimmate it'll over flow into the cup then drop back down again, continuing to rise and fall till it has more to collect. Kind of like washing your hair, lather, then rinse and repeat. When you clean the cup, (a third full is fine, a quarter inches is overkill and way too much work in my opinion) just turn off or unplug the skimmer. Clean the cup. Then just turn it back on and watch it for a minute till it settles into it's routine again. Then you have to be able to walk away, relax, and leave it to do it's job.

I hope I've been of some help.
What am I speaking Swahili? I appreciate the response, Silverado, but I've been doing this since the 70's and I've had a protein skimmer for 10 years. This is definitely not New Baby Syndrome. Let me go over this again, point by point.
1. The skimmer was working fine. It was perfectly dialed in
2. It was pulling out skimmate
3. Suddenly about 2 weeks ago, the water level started rising and falling dramatically, up to 5"
4. I was emptying the collection cup 4-5 times a day not because I'm being anal. I am doing it because the skimmer will sometimes overflow, washing the skimmate back into the sump, so I am keeping it clean whenever I'm going to be away from home. This way if it overflows it's only fairly clean water washing back into the sump.

As for your suggestion that I raise the water level a "quarter turn" at a time, believe me, just looking at the pipe makes it rise. I'm being facetious, but seriously, micro tweaking this thing changes the water level by 2". And it doesn't turn smoothly so it's not like I can grab it with two fingers and slooooowly turn the pipe. I have to grab it with my whole hand and ever so slightly jar it to the left or right.

Again, look at the picture. The water level is below the lower blue line after being set right at the upper blue line. I'm not talking foam, I'm not talking bubbles. I'm talking the actual water level. When it's that low it absolutely will not lift any skimmate out of the skimmer and into the cup. I tried leaving it like that for hours and when I got home it hadn't moved, but there was grunge on the inside of the skimmer wall so it definitely had stuff to remove. That didn't get the water level to raise to where it should be.


Well-Known Member
Hey. Took a shot at it. Have you tried changing the pump? Maybe its time. How old is it anyway?

And in answer to your first question: I don't know. What does Swahili sound like? o_O:)
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Sounds like a manufacturer related issue. Call Eshoppes and check with them. See if they have had similar issues and what they might have done to fix it.

Those pipes that you turn can be very difficult to dial in right. I had one on a sea-cone skimmer (cheap off brand) and I had some similar issues. I ended up getting a different skimmer in the end.

Just a suggestion, but you might could use some o-ring silicone grease (non-toxic for aquariums) and put a little on the inside of the T and a little on the pipe and see if it gets any smoother and if it is easier to dial in.

Even though your setup is new, go ahead and check the pump for debris, just to be absolutely sure.


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How deep of water is your skimmer sitting in? Is your output to deep and maybe causing back pressure or "back log"...This would cause the water level to drop in the body and make dialing it in a very precise thing. The tiny lefty loose is a big drop all of a sudden.

Imo needle wheel mesh wheel common cone skimmers r piles. Recirculating, air venturi, simple downdraft airstone/air pump skimmers works best.

The idea of a skimmer is to re create the foam on the beaches u see. The cone skimmer pushes and pushes foam out the top. Not getting much contact time and ruins pumps. It's better to have skimmer foam head get heavier and build up the neck.

Skim wet will get all the dissolved organic compound. Proteins are clear. The reason it's green is from the algae and zoo phyto ect. Skim dry will get detritus and the things YOU want to see out....just don't forget the things u can see.

My .02.


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If there has been no changes in the water, and your water level in the sump is constant, your skimmer should perform consistently. PH and temperature can have some effect on skimming performance, but it shouldn't change your water level... only the foam height. It sounds like a malfunctioning pump to me. Have you disassembled the pump to make sure the venturi and needle wheel isn't clogged with foreign matter? It happens. Also, make sure there are no bubbles getting sucking into the pump. When you clean the cup and neck, do you use any soap or chemicals? A simple sponge and fresh water is all that is needed, so you don't remove the biofilm that coats the surfaces and prevents the bubbles from popping prematurely. It took me a while to realize that bubble height is NOT the water level. I found this out by accident when I was working on the back side of my refugium, and light was shining through the skimmer. It was then that I noticed where the water level stopped, and the actual foam began. I lowered my water level to the recommended level, and it started working perfectly. If your skimmer has a water level line, shine a light from the back of the skimmer and set the water level to this line. How deep is your skimmer sitting in the sump? 8" seems to work best for most people. If the needle wheel and venturi are clear, check the impeller magnet to see if there are any scrub marks. If it uses a steel shaft, check for warping, or a cracked or broken ceramic shaft. If the water level in the sump is consistent, but the water level (not the foam level) in the skimmer isn't, then the signs point to a pump malfunction. Foam fluctuations are typically caused by something being introduced into the water column. Oils from excess feeding can cause a reduction in foamate, while the residue from marine epoxy can cause extreme excess foaming. Again, if the external water level is consistent, and the skimmer's internal water level is fluctuating, it may be time to contact the manufacturer about a pump replacement...

Edit: I just noticed where you said not foam, not bubbles, but water... doh!