Reef Aquarium Cleaning 101

Having a coral reef aquarium in your home or business is one of the most alluring, relaxing, and esthetically pleasing decisions you can make. The eyes of anyone entering the room with a reef tank are immediately drawn to the motion and color of the coral polyps and fish and for some of us, it is very difficult to peel our eyes away. However, without regular, proactive cleaning and maintenance, a serene coral reef display can quickly become a real eyesore. The best approach for making reef aquarium cleaning easy is to plan on doing a little of it on a near-daily basis, which allows you to keep your coral aquarium looking great for small investments of ten to fifteen minutes. Procrastination on maintenance will quickly lead to tedious slogs lasting much longer and requiring a lot more effort. So, to promote the former and help prevent the soul-crushing latter, here are some easy, proactive steps you can take for cleaning your reef aquarium properly.

Algae Scrubbing

As tedious as it may occasionally be, algae scrubbing is one of the immutable Laws of Coral Keeping. The same conditions that facilitate the growth of the gorgeous coral species in your tank are also ideal for a near-endless variety of algae, which must be carefully removed from the glass or acrylic viewing panels of your display or they will simply take over. There are many different types of tools available for algae removal but another of the aforementioned immutable laws is that the tools that appear to require the least amount of effort will probably result in the least effectiveness. Some of the tools that professionals rely on include white scrubbers on the end of handles, Dobie™ and Magic Eraser™ scrubbers sold for dishwashing, rigid plastic blades on the ends of poles, and occasionally, magnets with a soft felt side to protect the outside of the display and a moderately coarse side for scrubbing the inside.

To expedite algae removal and make this much faster, easier, and less tedious, here are a few ideas:

Develop a system – Start in one of the upper corners of the tank and divide each panel on the display into zones, focusing on cleaning all of one zone before moving on to the next. Methodically scrub each zone using as much of the scrubbing area as practical with your hand scrubber, as you can cover a lot more area quickly and efficiently. Then, move on to the lower parts with your longer tools. You will likely find that some types of algae require a lot more effort to remove. Try to get as much leverage as the space will allow and consider using one of the corners of your scrubber to focus on the stubborn spots.
Divide and conquer – To make this regular task fast and easy, consider focusing your efforts on one panel of the display each day, rather than taking on the whole tank in one session. This prevents coralline and other stubborn algae species from getting established and becoming much more difficult to remove.
Pay close attention near the substrate – It’s easy to zone out and become distracted when scrubbing algae and accidentally pick up a small chunk or chunks of the substrate in your scrubber. If you’re not paying close attention, these chunks can scratch the daylights out of your display (even glass), resulting in horror, nausea, self-loathing, and despair. Pretty much all of us have done this at some point. To safely get the algae right above the substrate, use a tool to gently move the substrate away from the panel and then go right after the algae.
Acrylic cleaning – Many reefers prefer acrylic to glass but it comes with additional considerations. As acrylic is much softer than glass, you have to be very careful with the tools you use and how you use them to prevent scratches and clouding. Even “acrylic safe” scrubbers can mar the appearance of acrylic, so exercise extra care at all times when scrubbing acrylic.

Pro Tips

Scrubber paranoia is your friend – Get in the habit of checking your scrubber on a regular basis to ensure that you haven’t inadvertently picked up a chunk of substrate, snail, limpet, or any other object that will scratch your display. By the time you actually feel a small chunk of something in there, it may be too late.
Plan on making your own tools – Professional aquarists fabricate their own cleaning tools all the time with PVC pipe, zip ties, scrubbers, and other materials. If there’s one spot in a back corner that you can’t safely or easily reach, make a tool that can get you there.
Be patient and careful – Scrubbing algae is one of the most perilous risks to your corals because while you’re focusing on getting that last little speck, you could be millimeters away from inadvertently bumping one of your corals and weakening or breaking months or years of growth in an instant. Pretty much all of us have done this at least once, too.

Water Changes and Substrate Cleaning

Some coralheads swear by regular water changes to proactively maintain optimal water quality parameters while others absolutely loathe them and go to great lengths to prevent having to do them. Much will depend on the type of reef system you have, the amount of money you’ve invested in dosing and automation, and other factors but if you’re just getting started with reefkeeping, you’re going to have to change your water occasionally to keep nitrate (NO3) and phosphate (PO4) under control. You’re also going to want to vacuum the substrate in your display to prevent the buildup of fish poop, uneaten food, and other detritus from accumulating and creating hypoxic pockets of hydrogen sulfide (H2S.)

First, shut off your system pump and powerheads before starting to vacuum the substrate and siphoning water from the system. If you don‘t, your sump will empty and your pump, powerheads, and perhaps your protein skimmer will run dry, none of which are desirable. Then, carefully place your gravel vac in a secure spot in your reef tank and induce the siphon by sucking on the end of the hose. When you can see the water coming through the hose, place the end in a sink, floor drain, or reservoir and start vacuuming your substrate.
With one hand, move the gravel vac slowly up and down in your substrate, keeping a close eye on how high the substrate rises in the vacuum tube. With the other hand, keep the hose between your thumb and fingers and apply pressure to increase or decrease the amount of water being siphoned from the system. If the substrate gets too close to the top of the gravel vac, apply pressure to the hose, stop most or all of the siphoning, lift the vacuum a bit and let gravity put the substrate back where it belongs.
Systematically move the gravel vac throughout the substrate concentrating on one spot until the water runs clear. Then, move on to the next spot until the targeted zone or all of the substrate has been cleaned. Take extra care near the base of live rock, as you’re removing the substrate, which could cause the rockwork to shift and fall.
Using buckets or another method, move new water from a reservoir of premade and well-aerated makeup water and carefully add water back to the system, taking care where and how you add it. Most reefers have a designated small submersible pump connected to a flexible hose that they drop into the makeup water, secure the hose in place, and plug in, allowing the pump to do all the work. Some coralheads with plumbing skills simply open and/or close a valve or two and move their makeup water back into the system that way.
Fire up your pump, powerheads, and skimmer and carefully monitor water levels throughout your system to ensure that water levels are right where they should be. The order in which you do this might not matter much or it might be important. Much will depend on the specifics of your system.

Pro Tips

Your mileage may vary – Your water chemistry parameters will inform your decisions on how much of a water change to perform and how often. Lots of reefers in forums say do x percentage of a water change every month and you’ll be fine. Take this advice with a large grain of skepticism, as everyone’s system, maintenance schedules, and water quality vary. In time, your water quality test results will tell you how much or how little to change and how often.
Be extra cautious – Take extra care when doing a water change and gravel vacuuming, as we tend to focus on the gravel vac and not where our hands or the hose are at any given time. It’s very easy to forget where you are in relation to the delicate skeletons of your corals and accidentally bump and break months and years of coral growth in an instant.
Watch out for black pockets in the substrate – if you see a black seam or layer in your substrate, it’s likely a pocket of detritus, which has decomposed and created a hypoxic or anoxic area full of hydrogen sulfide. When disturbed, this can be deadly to your fish and invertebrates. Regular gravel vacuuming will prevent these from forming but if you see one, make sure that your corals and critters are well away from the area when you target it with the gravel vac and carefully remove it from the substrate while taking great care to prevent it from releasing it into the tank.

Water Quality Testing and Tracking

For reefers, knowing the current water quality (WQ) parameters in their system(s) is more than a bit of an obsession. These numbers indicate the overall health of the system, how much or how little key parameters such as calcium, magnesium, and carbonate hardness are being metabolized by their corals, and how much nitrate and phosphate have accumulated in the water, which inhibits coral growth and health. How you go about testing the water is entirely up to you and your budget. There are many options, such as:

Drip or titration tests from API, Red Sea, Salifert, Hanna, LaMotte, et.al.
DIY all-in-one test kits from Mindstream, Trident, Seneye, et.al.
Other companies that accept water samples from reefers and provide detailed profiles of the water chemistry

No matter which method best suits your needs and budget, the salient point is to test your WQ regularly and record the results. The exact testing methodology varies by brand but the importance of tracking the results does not. Recording your WQ parameters for future reference allows you to:

Better understand reef chemistry and how your water changes positively (or negatively) affect this or that parameter.
Get a snapshot of the overall health of your system and everything living in it.
Determine how much or little to adjust any dosing you may be doing on the system.
Anticipate and proactively manage how much calcium, magnesium, and alkalinity you need to add to your system so that they are available in the correct ratios to your growing coral colonies.
Gain keen insight into how a WQ problem may have occurred and how to spot trends that will help prevent it from happening again.

Simply put, the importance of WQ testing and tracking cannot be overstated. Whether you use a notebook, an Excel spreadsheet, an app on your phone or another method, sooner or later, you’ll be glad you have those numbers to reference, guaranteed.

Mechanical Filter Cleaning

Whether you use a mechanical filter sock, a layer of filter floss, a pad with floss and carbon, or one of the newer roller filters that scroll at programmed intervals, the better you take care of your mechanical filtration, the healthier your system and animals are going to be. The uneaten food, poop, and other detritus floating around in your water and trapped by your filter will quickly begin decomposing and turn into ammonia (NH3), which is toxic to your fish and inverts. So, plan on cleaning your filter at least once a week (twice a week is even better.)

Filter floss or sock in the sump – Turn over (or, in the case of a sock(s) turn inside-out,) the filter and blast the funk away with a hose or running water in a sink. Then, turn it over and aggressively clean the other side. The more funk you can remove, the more effective and efficient your filter will be. Some reefers have extra socks and throw their filters in the washing machine for a more thorough cleaning.
Filter in canister filter – This will vary somewhat depending on the brand and build but before removing and cleaning your filter, take extra care to note how everything fits together properly. Clean with a hose or in a sink and put it back in the canister.
Filter in hang on back filter – Not many reefers use these anymore but if you have one or more on your system, you should be able to remove and clean the filter while the filter is still running. Better still is unplugging the pump and giving the whole filter a good cleaning right down to the impeller blades each time to keep the filter operating at maximum efficiency.

Pro Tips

Have some extra filters on hand – This makes it fast and easy to keep your filters clean and gives you options when they become thin and worn out.
Filters in sumps under the tank are easy to forget about – Out of sight – out of mind. If you’re prone to forgetting, set a regular reminder on your phone or another device to help you stay on top of this. It’s very important to keep your mechanical filtration clean.
Clean the mechanical filters on a regular basis – This will also help you understand how effectively you’re feeding your system and how much food you’re feeding out each time. If you’re finding a lot of uneaten food in your filter, consider reducing how much you’re feeding and/or changing how you’re feeding the system.

Protein Skimmer Cleaning

Whether you call them protein skimmers, foam fractionators, or something else, your skimmer is an essential life support component for keeping your water as clean as possible. Skimmers work by removing dissolved organic matter from your water. How you disassemble and clean your skimmer will depend much on the make and model but for the purposes of this article, we’re going to assume that you have a skimmer where the microbubbles are created by a needle wheel impeller. These are the most popular types of skimmers for hobbyists and are fairly affordable. Beyond removing the skimmate from the collection cup on top, how often you clean your skimmer is up to you but taking it apart and cleaning it once a month is a good idea for optimal skimmer life and performance.

Unplug the skimmer and remove it from the sump – Carefully disassemble it and place the components in a slop sink or similar area that you don’t mind coming into contact with concentrated fish poop. Take extra care of how you remove the pump from the skimmer body.
Clean each component – Use an old toothbrush, dishwashing scrubber, or weapon of choice and place each on a clean towel on the counter after rinsing.
Disassemble the pump – Carefully remove the spindle with the impeller and magnetic cylinder and clean every surface with a toothbrush or bottlebrush. Look for strands of filter floss in the needles of the impeller and remove them with tweezers or similar tools. Take extra care when handling this assembly, as the shafts are often made of ceramic, which is fairly brittle and unforgiving of getting dropped.
Make sure to also clean the chamber where the impeller spins – Biofilm accumulates on the walls of this chamber, along with the magnetic cylinder, which creates drag and reduces the speed at which it spins. Which, in turn, greatly reduces how many bubbles are getting ripped into the water.
Reassemble the pump and skimmer – Place it back into your sump and fire it back up.

Pro Tips

It’s common to make minor adjustments to the skimmer to keep it operating at maximum efficiency. If over time, you find that you can’t adjust the height of the foam crown anymore or turn the adjustment knob, your impeller shaft and pump chamber are probably fouled by biofunk and cannot turn nearly as quickly anymore. Take the skimmer and pump apart, aggressively clean the funk off the impeller and out of the chamber and you should be good to go. Just be ready to back off the adjustment knob quite a bit when you plug it in!
Cleaning the walls of the fractionation chamber regularly will increase the efficiency of the skimmer by removing the drag the concentrated poop causes as it accumulates on the walls of the chamber.
Simple skimmer designs are usually more efficient and much easier to clean. If you’re fairly new to reef keeping, don’t be seduced by skimmers with tapered fractionation chambers that look like a flower vase or overly ornate designs. Your skimmer will only look pristine when it comes out of the box or after a good cleaning. The fancier it looks, the more difficult it probably will be to clean and the more difficult it is to clean, the less likely you’re going to want to deal with it.
It’s not a bad idea to oversize the skimmer a bit based on the system volume. If, for example, you have a 250-gallon reef tank, consider buying a skimmer that’s rated for a 350- or 400-gallon system. As long as it fits in your sump, you’ll never regret this decision.

Pump and Powerhead Cleaning

Just like skimmer pumps, over time, biofilm collects in the volute (chamber where the impeller spins and pumps the water back into your display) of your pump and in the impeller chamber of your powerheads. The more biofilm there is, the faster it accumulates and the more it reduces the output and efficiency of these components. In the case of your system pump, this can become a moderately serious consideration, as if the output of your pump is reduced, the turnover in your system and how often your water passes through your filtration is also reduced.

For powerheads, remove them from your system, carefully disassemble them and clean them with an old toothbrush, bottlebrush, or similar tool. Once cleaned and rinsed, place the components on a clean towel and reassemble each powerhead. Doing this every two to three months should be sufficient.
For pumps, whether you have an AC magnetic-drive pump or one of the newer DC pumps, the approach is pretty much the same: carefully remove the screws holding the cover of the volute in place and take the cover off, noting the orientation of the cover. Then, carefully remove the impeller and inspect it for signs of wear like chipped blades or shallow grooves in the cover of the magnetic cylinder. Look into the impeller chamber and also look for signs of wear, such as small raised grooves often caused when the pump runs dry and friction heats up the plastic.
Clean the surfaces of the impeller, volute cover, and impeller chamber with your weapon of choice, rinse them, dry them all and reassemble the pump, taking care to tighten the screws in a star pattern. This should be done at least once a year. Twice a year is better for optimal pump life.

Pro Tips

It’s a very good idea to have a backup pump to swap in for emergencies or replacement pump parts. If your pump fails for some reason, you have just a few hours to get water moving through your system again before all kinds of bad things start happening (i.e. horrible water chemistry, ammonia spikes, dead and sickened fish and inverts, etc.)
Tightening the screws of your volute in a star pattern allows you to tighten the cover evenly, preventing leaks and cracks in the volute cover.
Don’t over-tighten the volute screws. Volutes are usually made of plastic and won’t tolerate the extra tension for very long before they crack and fail.
Use a label maker to leave yourself reminders of the last time you cleaned your pump. It’s easy to forget the last time you cleaned that puppy. If there’s a sticker on it, you know exactly when it was done and it’s an easy reminder each time you’re doing system maintenance.

As you can see, there are lots of considerations for how to properly clean a reef tank. Hopefully, some of these coral tank-cleaning tips will help you stay on top of cleaning and maintenance and prevent you from making some of the common mistakes we all make when cleaning our coral aquariums. As stated early in the article, the more proactively you work to stay on top of these essential tasks, the easier and less time-consuming they will be. Regard coral aquarium cleaning as a labor of love and you’ll be much more likely to do it even when you’d rather hit the couch and watch TV. Besides, when you’re cleaning and looking at your reef display from different angles, you’re much more likely to see the small details that make reefing so rewarding. So, crank up the tunes and get cleaning! You’re going to love the way your tank looks.

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