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Reef Equipment

Skimmer in Saltwater System

What do I need?

Protein Skimmers Are Key to a Clean Aquarium

Protein skimmers are an important part of filtration for the modern marine aquarium. Protein skimmers, or foam fractionators as they are technically referred to, are excellent for the removal of organic waste from the aquarium water. In a skimmer, large volumes of water are mixed with air under pressure to produce waste laden foam that is removed from the tank. The structure of these organic waste molecules makes them gather at the interface of the air/water mixture. This can be seen as an oily or hazy film on the water's surface in a nutrient rich aquarium. Protein skimmers utilize the process of foam fractionation to remove organic compounds from the water. This process involves the mixing of the aquarium water with an enormous amount of very small air bubbles in a reaction chamber, which provides a great deal of air-water surface area for organic compounds to adhere to. These extremely fine bubbles can only be achieved in the higher density salt water, which is why protein skimming is almost exclusively a filtration device for the marine aquarium. A protein skimmer removes waste before it would otherwise be degraded by bacteria in the nitrogen cycling process ultimately producing nitrate.

Invest in a Good Skimmer

Over the years skimmers have become complex and expensive. It is important to do your research and invest in the best skimmer for your sized tank that you can afford. Advice from fellow reefkeepers is critical.

While there are several design mechanisms for producing micro-bubbles in a skimmer, such as Beckett-injection, downdraft, and air-driven, the most common design for home-aquaria sized skimmer is the needle-wheel. In this common design, water and air are drawn into the skimmer body via a pump equipped with an impeller made with many cylindrical protrusions, the needle-wheel impeller. The needle-wheel chops the incoming air into very fine bubbles, producing such a high density of small bubbles inside the skimmer that the body of the skimmer appears white rather than clear water. Inside the skimmer the organic waste laden bubbles rise into the neck of the skimmer towards the top and the waste collection cup, while the filtered water exits close to the bottom of the skimmer. Usually a bubble-plate is located inside the skimmer body. The bubble-plate reduces the turbulence inside the skimmer so the bubbles rise to a more stable head of foamy froth. A wedge-pipe, gate-valve, or some other methods are used to control the rate at which water can exit the skimmer body. This allows the water level inside the skimmer to be controlled so that the proper amount of gathered organic waste, termed "skimmate", can be collected inside of the skimmer's collection cup. If the water level is set too high, termed "wet-skimming", the collection cup fills with watery waste too quickly, and may even overflow. If the water level in the skimmer is set too low, termed "dry-skimming", waste may begin to gather inside the skimmer walls and not even make it into the collection cup. The actual accumulated waste level inside the skimmer is affected by many factors including surface tension and barometric pressure, so the water level inside the skimmer may need daily adjustment to maximize waste removal.


Regardless of the Type, Keep it Clean

Skimmers may need some adjusting to maintain the proper water level. This may be due to inclement weather where lower air pressure affects performance, or instances when something that causes drastic changes in skimmer performance is added to the aquarium such as two-part epoxy or oily foods. It should also be noted that new skimmers may require a break-in period of up to several weeks before they perform consistently. When properly set, a dark brown sludge will gather inside of the collection cup, effectively removing organic waste from the aquarium water.

The collection cup should be cleaned regularly to ensure proper performance from the skimmer because waste building up inside the skimmer neck prevents the capillary action of the foam rising and overflowing into the collection cup.

Needle-wheel skimmers can be "hang-on-back" for aquariums without a sump, "internal" for use placed inside a sump, or "external" in which they sit outside of the sump. Internal protein skimmer should be placed in a section of the sump that has a consistent water level not affected by evaporation in the aquarium, the ideal water level varies based on the skimmer make and model. External skimmers require an additional pump to feed water into the skimmer.

Accessories such as automated skimmer neck cleaners, or waste collection vessels with a float valve to shut off the pump when full, allow for the skimmer to maintain peak performance for longer intervals between cleanings. Care should be taken with hang-on-back and external skimmers to ensure that if the skimmer were to act up the collection cup does not quickly overflow and spill saltwater onto the floor. With some skimmer designs, the use of a waste collection vessel equipped with a float valve that controls power to the skimmer pump is highly advised. In addition to the regular cleaning of the protein skimmer collection cup other maintenance of the skimmer include the removal of salt build-up on the air intake of the skimmer. An area where salt commonly collects and impedes performance is in the nipple where the air intake hose attaches to the pump. The head of the needle-wheel impeller should also be checked regularly to ensure it is not clogged with detritus. The skimmer pump should be maintained regularly just like other pumps on the aquarium. Any calcium and scale buildup inside the pump cavity and on the impeller should be removed by running the pump in a weakly acidic solution such as white vinegar, be sure to rinse well before returning to service. The entire skimmer body can be taken apart and cleaned if needed.

Type of Filters and Equipment

Power Filters

Power filters, also known as canister or hang-on filters, are often used on aquariums for filtration, but are not generally recommended as the primary filtration method for a reef aquarium. A small power filter may be used to hold activated carbon that is used to remove the toxins and yellow color that builds up over time in the water. The carbon should only be a high-grade reef aquarium carbon and should be removed and rinsed weekly and replaced monthly. The use of activated carbon is beneficial in the removal of dissolved organic material and should be used constantly or at least for a day or two each week. Other materials sometimes used in power filters are resins that remove phosphates or nitrates from the water. These are OK to use on a spot basis for problems but should not be relied upon as long-term solutions for phosphate or nitrate problems. The use of purified freshwater will often eliminate these issues, as well as careful feeding and watching stocking densities. Any material used in a power filter should be rinsed weekly to help lower the number of aerobic bacteria to reduce nitrate production, these materials are used for adsorption of certain compounds and are not to be used for biological filtration.

Power filters do have a use, such as for a quarantine or hospital tank. A bio-wheel type is good and you can put the bio-wheel in your main system sump for a while before you need the quarantine tank to seed it with bacteria.

UV Sterilizer

UV Sterilizers

Another method of water purification is UV light purification. The basic theory is that tank water is passed through a glass tube that is surrounded by UV lamps that destroy organic matter as the UV light penetrates the tube and comes in contact with the water.

UV sterilizers are often used in fish systems to help control parasites since the UV light will kill free swimming stages of parasites. The UV light will also help kill algae that is in the water and UV is often used on ponds. UV sterilizers do have their place in reefkeeping, but are not a necessity for the average reef aquarium. 

A couple of issues adversely affect the performance of UV units. UV lamps are at the core of a UV sterilizer. The effectiveness of the unit is directly proportional to the wattage of the UV lamp and if the water has contact with the light generated by the lamp. If the lamp wattage is too low or if the glass tube is dirty then not enough UV light penetrates through the water to be effective. 

It is important to buy a unit larger than you think you need and one that has a built in wiper to be able to clean the glass tube frequently.



Ozone is method of water purification that in fact does a good job even with small units available to marine aquarium hobbyists.

The theory here is that an ozone generator produces ozone on demand and is injected into the water, usually via a protein skimmer air intake, and the ozone oxidizes waste and organic matter in the water.

Ozone produces very clean and clear water and removes the yellow tint that inevitably builds up in your water.

Usually it is best to incorporate the use of ozone with an ORP controller. ORP is short for oxidation-reduction-potential and is a good indicator of water purity. The controller is set for a certain level and then it turns the ozone generator on and off as needed to reach that set point.

Small ozone generators are inexpensive and do a good job on many sized tanks. Small polyp stony coral systems need pristine conditions and ozone is an excellent addition to other filtration methods for these systems, it may make systems for soft corals and some larger polyp stony corals too clean and these corals may not do as well with ozone.

Under Gravel Filter

Under Gravel FIlter

I have been in the marine aquarium hobby since 1968 and in those days we kept fish only tanks, no live corals and only limited inverts.

At that time we understood the nitrogen cycle and the importance of bacteria in water filtration. The use of undergravel filters was popular and they worked quite well for the aerobic bacterial processing of wastes. Unfortunately, they are also nitrate factories constantly producing massive amounts of nitrate because the basic theory behind them is to constantly move aerated water through the substrate where aerobic bacteria can flourish. As the bacteria break down the waste from tank inhabitants they eventually produce nitrates. While nitrate is less toxic to marine animals than ammonia or nitrite, it still is not desirable and especially in a reef aquarium where much more intense light levels would lead to severe algae blooms if nitrate levels are elevated.

The only way we could control nitrate levels was to change massive amounts of water weekly and this became old quickly, especially when you had numerous large tanks as I did over the years. Bottom line, under gravel filters have seen better days and I do not recommend their use in a modern reef aquarium. However, they can be used successfully in a fish only tank with lower light levels and regular water changes.

Calcium Reactor


Media Reactors
There are many uses for reactors in a reef aquarium. Basically a reactor is simply an acrylic cylinder with a lid and connections for water to be pumped in and then returned to the tank. They may be designed as submersible in-sump units or stand alone units. The reactor can be filled with carbon, GFO, or other media designed to reduce nitrates or phosphates. The benefit of using a reactor is that the media is contained rather than in a mesh bag floating around the sump and the reactor forces water through the media and makes the best use of the media. Remember the nitrogen cycle, as the water flows through the media aerobic bacteria will grow and they will produce nitrates, so rinse any media weekly in freshwater and change at least monthly. 

Calcium Reactors
These are a specific type of reactor used to automatically dose calcium, magnesium, and maintain alkalinity. They are filled with calcium carbonate and magnesium media, typically sold separately in the form of rock rubble type media and magnesium pebbles. Carbon dioxide is injected into the reactor and when the pH of the water in the reactor is below about 6.5 the media begins to dissolve. The effluent from the reactor is saturated with calcium, magnesium, and carbonate ions and is dripped back into the tank or sump. Water is fed to the reactor by a small low pressure pump, typically a small powerhead. The reactor has a circulation pump that recirculates the water inside the reactor to maximize the dissolving of the media. The initial investment in a calcium reactor can be costly, but it does automate dosing and when magnesium pebbles are added it can be an excellent source for a larger and or heavily stocked tank. To automate the set up you would need a digital regulator for a carbon dioxide tank and a pH controller set up to maintain a range of pH within the reactor. The reactor has a port for a pH probe and the controller will automate the dosing of carbon dioxide into the reactor by attaching the digital regulator to the controller.



There are many types of pumps you can use in a reef aquarium including a dizzying array or powerheads used to increase flow within the tank (you can never have too much random flow in your tank--just think about how much is in the ocean), return pumps used to return water to the main tank from a sump, reactor and skimmer pumps, and others. Some pumps are submersible and others are not. The main thing to remember about all pumps is that they use an impeller that sits inside a shaft to move the water. When electric current is sent to the pump the impeller spins in the shaft and moves the water. Skimmer pumps usually have very specialized impellers that chop up the air injected into the skimmer into tiny bubbles. Over time dirt and calcium builds up in the shaft and on the impeller, unless this is removed the shaft and or impeller become deformed and eventually the pump stops working and is ruined. Once the shaft is deformed replacing the impeller will have no effect, you must buy a new pump. You can prevent this disaster by cleaning the shaft and impeller every month or two. A simple rinse and scrub with a toothbrush will usually do the trick. Do not use abrasives or tools because you can scratch or deform the shaft or impeller. If calcium builds up you can soak them in vinegar overnight to soften the deposits and then brush and rinse in freshwater. If the deposits are extensive then you can use muriatic acid with extreme caution to immediately remove any calcium. Be careful to use in a well ventilated area with gloves and eye protection and follow all precautions on the label.

Water Changes and Algae Filtration

Water Changes
Taking water out of your tank and replacing it with new saltwater is an excellent way to keep your tank cleaner and replenish elements: major, minor, and trace. You could keep almost any size tank without any dosing by doing small regular water changes, about 10% weekly. Some folks feel that doing water changes causes too much disruption to the tank inhabitants and they don't do any water changes. This can work if you are good about dosing all elements, but is probably not the best method for newer hobbyists. Regular water changes have been a reliable way of keeping a reef aquarium for decades and is still a solid practice I recommend.

Algae Filtration

Algae use nitrogen, such as nitrates, and phosphates as food. Incorporating macro algae such as Chaetomorpha or other colorful macros in your overall filtration scheme is very beneficial. 

You can add a refugium and have macro algae in that or add some to your sump along with a light source, even a small incandescent clip-on light will work. The algae will use excess nitrates and phosphates as food and remove them from your tank, once you remove the algae as it grows then you also remove the nitrates and phosphates from the system. 

Another way to use algae for filtration is to use an algae scrubber. These are sold commercially if you can find videos on YouTube on how to build your own. There are several ways of making one. You can make one out of screening and have water flow over the screen or have a reactor chamber and add macro algae and LED lights. However you do it, algae can be an excellent source for nutrient removal from your tank and help keep the tank more stable and clean.



I have kept many successful reef aquariums by using live rock and a live sand bed of about 1-2 inches deep. I use a good quality skimmer appropriate for the size tank operated by a pump that is more than adequate for that model skimmer. I recommend using high quality activated carbon on a continuous basis and making periodic water changes. The use of some macro algae as an aid to reducing nutrients can be very useful and can be incorporated in different ways. This should be all that is needed for most reef aquariums. Be aware that many reef keepers do not use a sand bed in their tank. Instead they rely on lots of water flow, up to 20 or more times the volume of the tank per hour, and a large skimmer to remove waste in the water. This bare bottom method does work well for tanks with predominantly smaller polyp stony corals such as Acropora. It may not be the best option for a mixed reef aquarium with soft corals and larger polyp stony corals. Small polyp stony corals can also thrive in systems with a sand bed and have for many years been kept by hobbyists with sand bed tanks also.

Sometimes you can find that you can over filter a tank, when I added ozone to one of the systems I noticed a sudden decline in the appearance of many of the corals, they looked less full and some just looked droopy and sickly. Upon stopping the use of ozone they perked back up within a few days. Some corals do not originate from such pristine environments and do not do as well when the tank is too “clean”. We can at times get too carried away with filtration and remove too much from the water. But again, ozone does work well in reef aquariums if used correctly, especially in small polyp stony coral tank where the desired result is very clean water.

Again, remember that there are many ways to reach the same end goal of a healthy and beautiful reef aquarium. There is no one correct way or wrong way and many folks have combined different methods and hybridized methods to reach the goal they desire. For a beginning hobbyist desiring an attractive mixed coral reef aquarium with a reasonable number of fish and invertebrates, the combination of live rock and a live sand bed with a good protein skimmer and periodic water changes is the best overall option of filtration.