A Refugium of sorts, this algae bed helps clean the oceans!

Building Your Refugium Clean-Up Crew

No one ever said that keeping reef aquaria is totally uncomplicated. Especially keeping them clean! Sure, some maintenance approaches are simpler than others; natural methods are, for example, fairly effortless means to control nuisance algae, detritus and pests.

Natural methods certainly require some research, planning and occasional monitoring; but for the most part, they involve adding organisms that improve environmental conditions simply by doing what they do… naturally. For you, this eliminates much need for tinkering with touchy equipment, changing expensive chemical filtrants, constantly algae wiping, etc. Plus, successfully creating a dynamic, self-sustaining ecosystem is hugely satisfying.

Perhaps the most common and most important agents of biocontrol for both algae and detritus are copepods. This should make plenty of sense, since these tiny crustaceans fulfill the same ecological role in most natural aquatic/marine environments. Increasingly, aquarists are taking all kinds of measures (e.g. phyto dosing) to ensure that their systems can sustain large copepod populations. Arguably, the surest way to promote high copepod density is to install a planted refugium.

Planted refugia (specifically the macroalgal “plants”) already have other, well-known benefits; they reduce dissolved nutrient concentrations, for example. These are considerable benefits, for sure. But planted refugia are worthwhile for their pod-promoting properties alone.

So–by cranking up pod numbers, a refugium helps to keep a tank clean. That doesn’t mean that the ‘fuge itself can’t get dirty. For example, massive accumulations of detritus can form in densely planted refugia. And pods can’t control pests. Like in the main tank, the best way to tackle refugium cleaning and remove pests is to adopt natural methods.

But planted refugia are necessarily different environments from the main tank. This means that many animals used for clean-up in the main tank cannot be used in the refugium. For example, urchins are excellent algivores that are great for the display, but can’t be in the ‘fuge because they’d eat all of the macros! There are just as many species that are safe with macros, but aquarists just don’t think to put them in the ‘fuge. Imagine what happens if you put a gazillion aiptasia-eating animals in the main tank but stock none in the refugium–you’ll probably never get rid of the aiptasia, right?

Again, overall, a refugium makes it easier to maintain a clean, healthy reef tank. But your tank will be even cleaner, with even less effort, if the ‘fuge houses its own clean-up crew.

Algaes working to help oxygenate and clean the oceans.For Algae

Obviously, planted refugia are brightly illuminated environments. Thus, even in such close proximity to their macroalgal competitors, nuisance microalgae can take hold there. It can grow on the glass, on the sand or even on the macros. A well-rounded group of algivores can control these bad algae. This must, however, not include any animals that might develop a strong taste for your macroalgae. Sure, some snails might eat some soft macros like Ulva, but it’s all good so long as they focus on the microalgae.

There are a few captive-bred snails that are suitable for this purpose. Not only are captive-bred trochus snails and siphonaria limpets both excellent algae-eaters but they also are much hardier than wild-collected specimens.

For Detritus

Particulate organic matter (POM) is highly prone to settling out in refugia (especially planted refugia) where flow is reduced and certain macros (especially meshy types like Chaetomorpha) act like mechanical filters. This isn’t necessarily bad. For one, it removes these solid wastes from the display tank, where they would otherwise be much unsightlier. Also, by settling POM in the refugium, it is concentrated in just the spot where most of the pods are (i.e. where they can eat it most efficiently!).

Still, in tanks with lots of well-fed fish, detritus can build up faster than the pods can consume it. This is where the pods can use some help. Detritivorous snails are perfect for this job. Again, because wild snails can be touchy, captive-bred specimens are a much better choice. Thankfully, the sludge-busting cerith snail and nassarius snail clean up crews are available as captive-bred. Tiny burrowing snails such as these significantly improve the appearance and water quality of a reef tank, and indeed refugium, by consuming organic wastes. Most of these also contribute to some film algae control as well.

For PestsAiptasia is a Common pest in the marine Aquarium

Many small invertebrate animals are used to control pests of various sorts. Most of these are quite happy to live in the ‘fuge. The list of pest control critters is a bit long to run through in its entirety here, but we’ll posit the peppermint shrimp as a great example. This is, for sure, due to its proven usefulness in eradicating a common and particularly nasty pest, the aiptasia anemone. But these shrimps are also pretty good at scavenging wastes in general. This would include larger chunks of organic matter such as fish food that might find its way into the ‘fuge. These guys can mop up in seconds what would take copepods hours to do. This is especially important when snails die in the ‘fuge; a peppermint shrimp will eat a dead snail long before it has a chance to decay and foul the water.


Your refugium clean-up crew may be built around your specific needs and specific type of system you have. But regardless of the details, it’s a really good idea to remember the ‘fuge when your stocking critters for algae, detritus and pest control. This undoubtedly will simplify your maintenance regimen and reduce your reliance on complicated, expensive filtration technologies. And of course your tank will be a whole lot more interesting to observe!

201 thoughts on “Building Your Refugium Clean-Up Crew”

  1. jason.prindle

    i thought that we WANTED to keep these things in the refugium, so i have never added a CUC to the refugium, rather give these pests a place to grow freely so they stay out of the DT.

  2. kathymiller9999

    Yes, this can be complicated get rewarding! With all the knowledge from Algae Barn, it can be done!

  3. Compy Ginorio

    I never thought of having snails in the refugium but I think that I will add some besides the pods.

  4. I have thrown a Mexican turbo snail in the fuge before… didn’t think of any other CUC. Will have to boost the crew!

  5. I will have to try some snails in the refugium and see if they help along with getting more for the tank.

  6. Excellent ideas.Will try snails and peppermint shrimp in my refugium. Assume they don’t mind the constant light?

  7. Mitchell Draehn

    Just built a sump for my new setup and will be adding some of these in the future thanks for the info

  8. The biggest issue I have with my clean up crew is snail poop it builds up so fast and is super ugly in a flat bottom tank. it’s a white ashy looking pellet and sinks right yo the bottom.

  9. Great article! It is very challenging to keep refugium clean! I definitely need to add more pods and snails.

  10. Great article! It is very challenging to keep refugium clean! I definitely need to add more pods and snails.

  11. kaylie.marcellus

    I’ve never seen peppermint shrimp before! They’re so cute. Complete ecosystems always interested me, especially the jar terrariums. I used to have a huge pest snail problem and then got a feeding dish and that’s helped me a ton, my cherry shrimp do the rest.

  12. kaylie.marcellus

    I’ve never seen peppermint shrimp before! They’re so cute. Complete ecosystems always interested me, especially the jar terrariums. I used to have a huge pest snail problem and then got a feeding dish and that’s helped me a ton, my cherry shrimp do the rest.

  13. bglover65-5383

    Clean up crews are absolutely essential for any saltwater tank. In any tank build-up, I start with the clean up crew and work my way up.

  14. Nathan R. Knowles

    I had an urchin in my refugium for a while. My macro algae still had to be trimmed up frequently. I think it liked the coralline algae covering the sump more.

  15. I’m looking forward to installing my first refugium soon. I have spent a lot of time researching what is best to use and it seems much more beneficial to the system than.a bunch of chemicals.

  16. Suggestions for clean up crew for a 220 gallon reef aquarium and a 125 gallon fish only aquarium and a 45 gallon seahorse aquarium

  17. saintdominick

    Wow there’s so many options to work with then. This minimized the amount of equipment needed to maintain your tank giving it a more natural look. I think I might switch to salt water. I don’t feel like I have as many options with fresh water. I learned so much just trying to apply for the contest. I honestly didn’t know that much about salt water tanks because I’m still pretty new to the hobby. Thanks

  18. This is some great info. My brother just got me into this hobby and now I am obsessed. I differently add this blog to my top five.

  19. Looks like I m going to have to put some critter in my fuge? Will they eat up on the copepod population?

  20. I didn’t know that I’m supposed to add snails to control the algae in there. I’m so glad that I read this

  21. As with anything in this hobby, make small and deliberate changes to address concerns/conditions so as to ensure positive outcomes. Always enjoy reading and learning from your articles. Thanks!

  22. Scott D Carpenter

    I have had many if these critters over the years but the best $30 I ever spent in my life was for an aptasia eating filefish. I had hundreds taking over my tank and tried Tha aptasia magic wand, laser and almost every other product to get rid of them. Couldn’t use shrimp because I have wrasse. The filefish ate the all in less than a month.

  23. Pingback: 6 Incredible Interesting Algae Facts You've Probably Never Heard About


    I don’t have a refugium in my current tank, but I have 4 hermit crabs, 2 emerald crabs, 2 sally lightfoot crabs, 2 peppermint shrimp, and a lawnmower blenny that help to keep my tank spotless.

Leave a Comment

Your email address will not be published. Required fields are marked *