This is a close up pic of the refugium sump for the two tier system.  It used to have red mangroves in there but the water level changes a lot and they died.  The light is still on because coralline algae is growing in there.  

This is a close up pic of the refugium sump for the two tier system.  It used to have red mangroves in there but the water level changes a lot and they died.  The light is still on because coralline algae is growing in there.  

Build Your Own Refugium Sump

This is the last of the blogs for the recent Care Guide update.  


A refugium sump doubles as your filtration system sump that contains your equipment and a refugium.  There are about 100 ways to build one and I’ll just give some general guidelines for you to follow and a couple of different examples.  Your design is up to you. 


What you will need:


A tank of some kind; this can be an aquarium, a strong plastic tote, or a tank you build from scratch.  I prefer a tank I can see through.


A light; a daylight spectrum 6500-6700k light is best for this. 


Some method of dividing the tank into chambers; this can be sheets of glass or acrylic with the appropriate bonding agents, (silicone or acrylic bonding agent) or it can be smaller tubs or containers that fit into the sump. 


Your filter media, this will include the three types of media mentioned at the top of this section, biological mechanical, and chemical. 


Your equipment; all of your pumps, skimmers, heaters, etc. necessary to make the system operate.




From the discussion on sumps you already know a pump will sit in your sump or in the plumbing that leads to it.  This pump will move water up to the main tank and the main tank will overflow into plumbing that leads to your sump.  So you have water flowing out and water flowing in.  You want these at opposite ends of your tank.  As the water flows through your sump, it will flow through all of the types of media you have in place.  It will also flow over your heater and it may get skimmed by your protein skimmer.  The path the water takes to get through all this media is up to you. 


The refugium in the sump is a large chamber that houses the life you want to protect from your fish.  Usually it is set up similar to an aquarium display.   This would include a substrate such as sand, live rocks, and possibly mangroves or macroalgae.  Remember if your sand is 3 to 6+ inches deep, it forms a low oxygen environment for anaerobic bacteria to live.  (Remember an advantage to deep aragonite sand beds is that they dissolve over time releasing calcium into your water.)  These bacteria consume nitrate.  Often copepods, worms, aiptasia, sponges, and bacteria will populate the refugium without any help from you.  You can also buy these items, either in bags or on life rocks.  Aiptasia is often a nuisance in your display tank but in your sump, it adds to filtration. 


The light goes on top of the refugium chamber.  Because the PH of an aquarium falls during dark hours, it is common to set a timer on the light such that the light comes on at night and goes off during the day.  Another option is to leave the light on 24 hours a day.  This is probably less efficient than having a light cycle but it is simple. 




However you design the path for water to flow through your system, always ask yourself, can this chamber get clogged? Where will the water flow if it can’t flow through this chamber?  Will it flow onto your floor?  To prevent this from becoming a problem, always build a bypass to any clogable chamber.  When the chamber clogs, the water level will rise in the prior chamber.  By not having that chamber’s walls reach the top of the tank, it will overflow its walls but not the external walls of the tank. 


Nutrient Lockup and Export:


The whole point of setting up a refugium is to get nutrients out of the water.  The life forms in your refugium do this by consuming the nutrients and making them a part of their biomass.  In the process of doing this they lockup the nutrients and prevent them from being available to nuisance organisms such as cyanobacteria that can cover your tank in a matter of hours.  A refugium has a limit to the amount of biomass it can house.  Once that limit is reached the organisms in your refugium are no longer able to lockup nutrients.  You can expand the lockup capacity of your system by feeding biomass from your refugium to your fish.  This locks some of the nutrients in the flesh of your fish.  It also reduces the amount of nutrients you import into the system by feeding fish foods from outside.  Many fish will eat copepods extracted from your refugium with a baster or by your system pumps.  Some fish will also eat macroalgae.


Once the lockup capacity of your whole system has been reached, it is time to export nutrients.  This is simply a fancy way of saying, take stuff out to make room for growth.  Mangrove trees can be trimmed like bonsai trees.  Macroalgae can be trimmed and given away or even sold.  Live rocks and sponges can be swished in a bucket of seawater to remove excess waste.  The substrate can be vacuumed, or sifted a portion at a time.  Filter fiber can be replaced.  Be careful not to export too much at any one time.  This could reduce your system’s lockup rate and cause fluctuations in your water parameters.  Also consider that when you clean your display tank, you are also exporting bacteria.  This combines the effect of any nutrient export you are doing in your refugium. 


Sometimes macroalgae can become toxic if it gets too crowded.  Always be mindful of how full your refugium is getting of macroalgae. 


Example 1:


The first example of a refugium sump is a 20 gal sump I have running on a 30 gallon tank.  This refugium could run a tank much larger than it is running but it is doing a good job.  It is made from a 20-gallon aquarium that is divided with glass panels into three chambers.  The first chamber is the refugium.  Often the first chamber is a mechanical filter.  This sump is fed by an overflow box that has sponges in it.  That acts as my mechanical pre-filter.  Next to the refugium is a media chamber.  Here I have an additional sponge, fiber filter, and a bag of carbon.  Notice that if the 2nd chamber overflows, it overflows into the 3rd chamber.  The third chamber is the pump chamber.  The pumps are protected from sucking up gravel by having a chamber all to themselves.  There is a heater in the refugium chamber as well as a protein skimmer. 


In this design, the water level in the entire system is relatively constant until the water level falls to the height of the wall separating the 1st and 2nd chambers.  Then the water level in the 1st chamber remains constant while the last two fall till the pumps suck air.  Because the capacity of the last two chambers is much less than the system as a whole, if I see the water level is lower in the last two chambers than the 1st chamber, I know I need to add water immediately.  By keeping the heater in the refugium chamber, I know it can never go dry. 


The walls forming the chambers are not perfectly vertical.  They are put on an angle so that the 2nd chamber is narrower at the top than at the bottom.  This is so the sponge can’t float up. 


Example 2:


The second example is a 37 gallon aquarium that I didn’t want to permanently divide.  It’s a nice tank that I may want to use as a display one day.  The tank has two chambers.  One houses all of the mechanical and chemical filtration media and the other is the refugium.  The heater and pumps both sit in the refugium chamber.  The pumps have shields around them to protect them from sucking up substrate and I have the substrate—crushed coral—pushed away from the pumps so they will sit lower. 


The first chamber is made from a dollar store garbage can I have hanging on the side of the tank.  The overflow from the two display tanks above it falls into this can, through the media inside, and out the holes I drilled in the bottom and bottom of one side.  There is pond filter media that is a hard plastic woven wire thing called Matala®.  There are 3 densities of this material.  A bag of carbon sits on top of the Matala® and a fiber pad sits on top of the bag.  The fiber pad clogs up with waste and I rinse it in the sink.   The garbage can sits lower than the sides of the tank, so if it overflows, it overflows into the refugium chamber. 


There isn’t much to explain about the refugium chamber.  It contains the crushed coral mentioned above, some rocks, and a few red mangroves.  The heater is down low in front, the pumps are off to one side.  The protein skimmer is not in the sump.  One of the pumps in the refugium leads to the protein skimmer and it dumps into the lower tank.  This allows the pump to perform two tasks at once.  It runs the protein skimmer and it provides circulation for the system.  As the water exits the protein skimmer, it flows through a second garbage can with Matala® and fiber but not carbon.  

Sumps and Refugiums

This is another section I wrote for the Coral Care Guide that has not yet been added.  



A sump is a tank of water that sits below your main display tank.  Usually it houses your system’s equipment and filter media.  Water is pumped from the sump into the display tank where it overflows into pluming that leads back to the sump.  The water level in the display tank is set by the overflow pluming, while the water level in the sump raises and lowers as water evaporates or is added to the system.  This is a nice feature that keeps your display tank full at the same level at all times. 




The root word refuge in the word refugium kind of gives you a hint as to what a refugium is.  A refugium is a place where vulnerable life is protected from harm from those that would do the harm.  In an aquarium a refugium is a separate tank from the main display tank where such life is kept.  Water flows from one tank to another and back in a cycle.  The water carries bacteria, and other microorganisms with it but it does not carry predatory animals such as fish.  


A refugium can be kept as a display tank to display less aggressive fish alongside more aggressive fish while running a single system.   More commonly, people use refugiums as part of the filtration system.  As stated in the section on cycling a new tank, there are many microorganisms and tiny animals that are important for completing the nitrogen cycle.  In a reef tank, some of these cyclers are copepods and amphipods.  Copepods and amphipods are a favorite meal of many fish.  Keeping a refugium allows their population density in your system to be much larger than it otherwise would be.   In addition to microorganisms one can keep mangrove trees or macroalgae in their refugium.  Both consume nitrates. 


There are two common ways to set up a filtration refugium.  One is to use a hang-on device.  This is very similar to hang on filters commonly used in fresh water aquariums.  Sometimes people even convert hang on filters into refugiums by removing the filter cartridges and using the empty space as the refugium tank.  The other common method is to put a refugium in a sump.  There are commercial refugiums of both types available on the market today however it is very common for people to build their own or retrofit a commercially built piece of equipment into a refugium.   

20 Gallon Refugium Sump DIY

Note: This blog is a little long winded.  The video at the bottom is worth a watch, even if you don’t want to read the whole thing.  

In the spring of this year (2011), I made a 20 gallon refugium sump out of a 20 gallon glass aquarium.  I did this because it was a lot cheaper than a store bought one and, because it was going to be visible, I wanted it to look halfway decent.  Sure you can see the pumps and filter sponges but the look of those acrylic sumps, with the tops folded over, just doesn’t appeal to me.  I think this one turned out pretty and sometimes I lay on the floor and stare into it.  There is so much going on in there that you never know what you will see. The new system is going to have a cabinet on the bottom. Maybe I should put a window in that cabinet.  

As you can tell from the root word to refugium, refugium provide a refuge in your aquarium system.  What is the refuge from you may ask?  It’s from predatory fish and coral.  This refuge allows things to live in your system that would otherwise be eaten.  Some refugiums are second display tanks that house fish or other life that would be eating by the fish in your main tank.  Others are used as filters.  Some refugiums are small tanks that can hang on the side of a display tank like a hang on filter does.  The word sump applies when the refugium is placed under the display tank.  Usually the word sump is left off but I feel it is more specific to use it.

This 20 gallon refugium sump has lots of things living in it.  There are several live rocks, which are covered in fantastic displays of coralline algae. There are several red mangroves; starfish, millions of copepods, aiptasia, snails, and a substrate full of bacteria.  There is also some read macro-algae growing in there, tube worms and some hardish inflatable thing.  Most of these little life forms will filter impurities from the water as food.  Aiptasia is often thought of as a pest because it can spread fast and prevent corals from having real estate.  In the sump, it can help filter the water.  The copepods are all the little bugs that are living in there.  Coralline algae is the purple that covers everything.  The starfish, I don’t know much about.  

Red mangroves absorb nitrates from the water.  It is said that they don’t grow fast and are not effective nitrate reducers.  I suspect this is because of the bonsai like fashion most people keep them.  I’m planning to experiment with putting a in a place where they have more room to grow.  I have a hard time believing that a tree, capable of growing to 100 feet, grows too slow to absorb nitrate from an aquarium of any size.   

I’ve taken a video of the sump.  The video shows some of what I talked about but not all.  I almost got footage of a tube worm flowering out of its tube but the chip filled seconds before it happened.  I did get a starfish but you can only see some of its legs sticking out of the mangrove roots.

I don’t think I need to go into how I made the sump because it’s pretty straight forward.  I will say a few things though.  The glass in the dividers was bought a glass shop and not the hardware store.  It is 3/16” thick, which is thicker than you can get in the hardware.  It is sharp and I wish I had them dull the edges.  Finally, the glass is intentionally installed on an angle, tapering the slot for the sponge narrower towards the top.  This is to prevent the sponge from floating up.  

Happy Reefing Everyone,


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Nov 22nd, 2011 11:22am 

Some coralline algae grows on a live rock in a 20 gal refugium/sump.  A video and text blog of this sump is soon to come.  Taken, 11/5/11 with cannon PowerShot sx110is.  
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Nov 22nd, 2011 9:24am

Some coralline algae grows on a live rock in a 20 gal refugium/sump.  A video and text blog of this sump is soon to come.  Taken, 11/5/11 with cannon PowerShot sx110is.  

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Nov 22nd, 2011 9:24am

Nice Protein Skimmer

I picked up the *protein skimmer for the new system on the way home from my day job the other day.  It’s a Beckett skimmer, which means it can process a very large volume of water.  This skimmer is perfect for this tank and should I want to put large fish in it, or heavily feed my coral in order to farm them, the skimmer will keep up.  It’s also great for SPS (small poly stony) coral which like low nutrient water.  Because Beckett skimmers use large pumps ((this one will use a 1200gph (gallons per hour) pump)) to operate, I plan to put the skimmer on a shelf with the outlet above the lower tier tank.  This way, I can make use of all that water flow and the 60 watts of power such a pump consumes 24 hours a day 7 days a week —even on Christmas.  What’s funny about this is that I designed the two tier stand to house the skimmer in the bottom.  I could have built the stand lower.  

Beckett skimmers produce micro bubbles that escape out the outlet.  To alleviate this problem, I have decided to make an overflow basket out of a Dollar Tree trash can.  This idea is based on an overflow basket that came with the Coralife that I have running on another tank.  

Here is a pic of me with the new skimmer.  I am 6’5” tall.

Above: It’s hard to see the name, so the skimmer is by Bashsea and it’s really a pretty piece of equipment that I won’t mind having out to be seen.  It’s called a Twisted Skimmer.  Here is the skimmer’s web page on the Bashsea web site.  I got the 6” X 30” model.  I’ve seen this skimmer working in a store and it works well—a lot better than the Coralife.  

Above: Here is the microbubble basket that came with my Coralife simmer.  

Above: This is the Dollar Tree trash can I am planning to turn into a microbubble basket.  It’s about 25% bigger than I’d like but for $1 and the right color/shape, I’m not complaining.  Thank goodness Home Depot only has black acrylic sheets online and in 4’X8’ sizes or I would have built a box for like $30.  Preview: I made a close up video, of that refugium, I plan to share and discus later.  It’s really something to see.  If you have questions about what you are seeing behind that can, they will be answered in that post.

Preview: Tomorrow, the 3/4” acrylic sheets I ordered from Laird Plastics should be ready for pick up.  I plan to build an 87 gal rimless tank out of it.  More on this later.  

Goodnight and happy reefing people.


* A protein skimmer is a device that cleans the water by making foam.  Dead bacteria, live too I suppose, and other dirty stuff that leads to nitrates building up in your tank stick to the surface tension of the bubbles.  The bubbles pop at the top and release their filth into the cup.  For an example of that filth, see this post and watch till after it says one week later.  There are several ways to get bubbles to form in water.  The Wikipedia page I linked to above does a great job explaining them further.  

                                      Nov 16th, 2011 9:55pm

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30 gal coral video

This is a video of a 30 gal long (36”) tank stuffed with coral.  I set this tank up as practice before I build my two tier system.  This tank will be converted into the sump for that system.  There is a 20 gal refugium sump below and not shown.  It has aragonite substrate, live rocks, and approximately 1.3 million copepods (just a wild guess.  I should put up a video of just the sump.  Maybe next week.  Most of the coral are listed on my web site, and each one is named, described, with care instructions.  I’m working on standardizing my description format to look like this listing for the brain coral but they don’t all look like that yet.  I think this format is easier to follow than the single paragraph I have on some corals.  If the video doesn’t embed like it is supposed to, you can view it here 

Happy reefing,




Sep 17th, 2011 11:40pm

Hi all new readers.  My name is Joe and I have been an aquarium enthusiast for about eight years as I write this in Sept of 2011.  I’ve been running planted systems for about eight years.  After great success with my main display, I was getting a little bored and decided to make the jump to marine systems about a year and a half ago.  Wow, it seems like it has been longer than that.  At this stage of the game, I have one 45 gal high planted tank.  That’s the one in my main picture.  I also have a 29 gal Biocube reef display and a 30 gal long storage tank with a 20 gal refugium sump.  I built the sump myself out of an aquarium.  The tank holds items for my online store.  I also  have various other dry tanks laying around awaiting projects or just put away for a while.

Next up on the agenda is the construction of a two tier holding system  that will have two 60 gal low tanks and a refugium sump.  More on this in my next post.