Should You Run Your Protein Skimmer Full Time Or Part Time?

The protein skimmer assists in the removal of dissolved organic compounds (DOC’s) from the water column. The protein skimmers manufactured nowadays are normally exceptionally efficient – as long as they are kept clean!

So what do I mean by running your protein skimmer full time or part time?

Well basically a protein skimmer which is run full time is turned on 24 hours a day 7 days a week whereas a part time skimmer is on for less hours in the day – 12 for example.

So why would anyone consider this?

You have to look carefully at what you are keeping in your saltwater aquarium. If you are keeping fish only then I would recommend without hesitation that the protein skimmer be run fill time. Fish produce a lot of waste and we have to feed them so the protein skimmer assists in the removal of these items as well as others from the water.

If you keep a coral only or a mixed reef tank then perhaps it could be different. I say the word perhaps as you need to look very closely at what you keep in your aquarium. The reason for this is that we are interested in the load on the aquarium i.e. how much waste is being produced which the protein skimmer can then process. In a coral only aquarium then very little bioload should exist as corals put very little strain on the system. This does not mean that you do not need a protein skimmer as I personally would never have a saltwater aquarium without a protein skimmer installed.

In a mixed reef aquarium then you obviously have corals and fish, therefore like the fish only aquarium the fish are being fed, due to the feeding waste is produced which could easily impact water quality. Yet, how many fish are in the aquarium? How large are the fish?

What you can do is review your protein skimmer over a couple of weeks. Ensure that you have optimum water quality and then check your collection cup at the end of the period and see how much waste has been produced. If the cup is over half full then realistically you probably need to keep the protein skimmer running full time to ensure that everything is removed. If the cup is less than half full then faesibly you could potentially use a part time skimmer.

Of course this is not set in stone as each aquarium system is different. The decision ultimately comes down to you based upon your particular setup.

So why do it?

There is a lot of debate as to how much good is removed by a protein skimmer as well as bad. As protein skimmers have evolved over the years they have become more and more efficient. Due to this efficiency they can remove a huge amount from the water. This is great in one way as it assists us in both creating and maintaining the water quality which our aquarium inhabitants require however what else is removed?

Personally I have absolutely no idea. I am not a scientist and do not have the tools, skills or knowledge to be able to analyse the output from a protein skimmer and see what it contained. All I know is that it is brown and exceptionally stinky!

It is believed that some of the items potentially removed by the protein skimmer is used by corals as food. Corals receive the majority of their energy from the lighting which is provided to them, however they do receive a good amount from food captured in the water. This could be the likes of phytoplankton, zooplankton etc. Have you ever watched a documentary on the television about natural coral reefs? Have you seen how many particles are floating about in the water? Loads aren’t there – in the aquarium we do not have this amount as we have to use man-made devices in order to keep the water clean.

So potentially if you run the skimmer part time some of this life will not be removed and can be used by the corals as food.

There have been reports that when this is performed it has been noticed that the corals appear to have better colour and better polyp extension.

Another method is by actually feeding the corals yourself. You can purchase various ready made containers full of coral food which you feed to the aquarium. There are also various methods you can follow to make your own coral food. I will cover coral feeding in a future article.

Would I do it? – maybe but only if I was absolutely positive that it was not detrimental to water quality and I would be testing the water all the time.

Would I recommend the beginner do it? – Probably not – not just because they are new to the hobby but the aquarium is also new and needs to age a bit. Perhaps if only corals were being kept but even then I think that it should be run full time until the aquarists gains experience.

  1. Something else to keep in mind: The protein skimmer is a major source of oxygen in the typical aquarium, particularly overnight when the bulk of photosynthesis has ceased. Cutting off the skimmer at this time can lead to a serious drop in dissolved oxygen levels and pH — both of which can stress tank inhabitants.

    This is unfortunate, particularly for those of us with daytime polyp extension problems… it’s hard to feed small-polyped corals during the day because their polyps are withdrawn and it’s hard to feed at night because of the aforementioned oxygen-level problems when the skimmer is turned off to facilitate feeding 🙁

    Andy’s last blog post..R.I.P. Anthias #3

  2. I just set up a 65 gallon tank like 2 months ago and It seems like its pretty much stable. It went through a phase where it grew a lot of hair algae all over the sand and then I put in my first creatures which was 6 hermit crabs and now there is no more hair algae and now I just have the lightly green algae that tints the glass so I bought a lawnmower blenny.He eats a majority of the algae on the glass and rocks but he cant seem to keep the whole tank clean. Should I invest in another one?

  3. Hello Andrew,

    A 2 month old tank will be initially stable (ie. the bio-filter will contain the necessary bacteria to deal with toxics) but it will still be ‘wobbly’ (a good technical word that!). Some aquarists come to grief at this stage as they think all is ready and stock too quickly.

    From what you say the crabs have dealt with the hair algae and the blenny is tackling the glass algae plus more but is not clearing everything. One of the jobs most (all?) aquarists have to do is clean the algae off the glass often about once a week. This is easy, especially using an algae magnet.

    Personally I would not obtain any additional algae eating livestock and see how things develop. It could be that as the tank fully matures the algae dies back anyway as nutrients are used up (especially if there isn’t any overfeeding and routine seawater changes are done). If algae reduction does occur then the food supply will diminish leaving not enough for all.

  4. Thanks John If you don’t mind I have a few more questions. Since I’ve set up my tank I have not yet changed the filter nor did a partial water change because I’m not sure if its kinda early for the first change seeing the tanks been set up for only 2 months and I have only had live rock in it for about 6 weeks and the 1 fish and crabs for 1 month. How can you tell is the right time for a water change? Also do you think the 1 gallon containers of distilled water at the grocery store would be good for the tank? Also do you know what wattage UV sterilizer I would need for a 65 gallon tank? And is there any secrets to making your live rock purple faster and mushroom reef multiply quicker?

  5. I’m afraid I don’t know what size the UV should be, but a check with the local LFS or at a manufacturer’s website should bring the information to the surface.

    Routine seawater changing is important as more and more livestock go into the tank. Stocking should be slow to permit the bio-filtration to adjust. If routine changes are not done routine seawater testing should highlight – eventually anyway – a fall in quality, such as increasing nitrates. I don’t think any harm will have come to your system to date. However, once livestock are in place then the seawater starts to deteriorate, so I would commence doing changes. The initial guideline is 10% of the total net gallonage in the system (so this includes any sump). The amount changed can be altered as experience is gathered of the system’s requirments.

    Distilled water could be used if it is of high purity, but it could be more economical over time to use an alternative, which I and many others use, this being a reverse osmosis (RO) filter. These produce typically 95 to 98% purity. They don’t cost that much, though I don’t view them as particularly cheap. They come in different ‘gallons per day’ outputs and one should be chosen for the size of routine seawater change needed.

    By ‘filter’ I assume it is a mechanical filter. The regularity of servicing is dependant on the state of cleanliness of the seawater. At first it is usually trial and error, just having a look to see what the condition is. I clean mine once every 4 weeks. As said, each aquarium is different. It is better to clean a mechanical filter too much than too little. I’m sure you know, but if you have bio-filtration in say a canister filter, the bio-media should never be cleaned in tap water or there’ll be dire consequences! Clean bio- media gently in warm tank seawater, say at a routine seawater change.

  6. Sorry Andrew I missed your point on live rock purpling and mushroom growth.

    The best way to generate growth of corals and coralline algae is to maintain high quality seawater conditions, and secondly to have the correct reef type lighting fitted. Nature will go its way if conditions allow.
    Corals could be increased by propagation but your probably not ready for this. Also, coralline algae can be increased by scattering broken bits over the rocks, but this is not intended to mean destroyinmg nice bits already on the rocks. When plenty has grown, sometimes bits fall off and these could be used.

  7. Hey John,

    How are you doing? I was wondering if I am on the right track but I have had my tank for last 1-1/2 year now. It was just a fish tank for last 14 monthes or so and I have had my protein skimmer running 24/7 till last 3 hrs. I realized that when I have coral I shouldnt leave it running. So well within last 2-3 monthes I have added, Zoo, hammer head coral and they have been doing amazing well. And last night I added Pulsing Xenia that I bought from a local reef keeper and it was nicely pulsing in his tank but now my xenia is not pulsing. So i started researching and came across the proteing skimmer over skimming so I shut my skimmer off and yea. Now what else should I do to make my xenia pulsing again. I have T5HO 36inches light fixture and T5 24 inches fixture. Your help will be very much appreciated.
    Thanks once again.

  8. Hello Jay. Having had a fish tank for a good while will have given valuable experience.
    Having corals in the tank doesn’t mean that a skimmer cannot run 24/7 – mine runs more on than off. However, the proof is in the pudding as they say….if your corals are doing really well there’s not a lot wrong! Some corals are able to make use of dissolved organic substances (DOC’s) so experimentation is often the way with the skimmer.
    The coral pulsing sometimes does stop even though in another tank it was active. I don’t know the real reason why the pulsing should stop – I’ve seen suggestions that it could be low oxygen content. I can’t really confirm this but an oxygen test could be worthwhile maybe? Also, the coral was transferred to your tank very recently and time for it to fully settle will be needed, the transfer will have been stressful.
    You sound to be doing really well.

  9. Hi, I only have a 29 gallon biocube , its pretty well stocked with mixed lps and leather corrals along with a couple blue damsels a red fire shrimp, a corral banded shrimp and various inverts. Everything is doing great but i was wondering if i should invest in a uv sterililizer or a protein skimmer. I do religious water changes every week. Which one would be more benificial. Thank you

  10. Hello Brian. First of all, I don’t really like the word only – nothing wrong with a biocube! Glad everything is doing well. A UV sterilizer is good but, personally, I would use a protein skimmer. They are affordable, easy to run and don’t need a lot of attention. They do become yukky after a while and it is important to clean the dirt out – easy. Mine needs attention about once a month though it varies. The skimmer generates lots of tiny bubbles and a fairly regular check will show it is still working.
    Glad you called. Enjoy the hobby – I’m sure you do.

  11. I’ve got a salt water tank and I just hooked up my skimmer, should I let it run all the time? I don’t like what it looks like. Like it’s all in one spot. I’ve had my tank about 4 months now.

  12. Hello. Most aquarists run their skimmer all the time. Some advanced aquarists turn it off for a period each day for specific reasons. The skimmer greatly assists in maintaining high quality seawater, the number one requirement. If you don’t like the look of it, then they can run separate from the aquarium. The one I run is a hang on type and the outflow runs down a slope with dark green algae on. The slope helps with oxygenation and I assume the algae removes some unwanted contents from the seawater. Skimmers need a clean from time to time, when the sides of the bubble tube is clearly miscoloured and dirty – an easy job.

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