Natural Reef Aquarium Method

best method for setting up a reef tankThere are many methods to create a reef tank. There is everything from just live rock and flow (no refugium, protein skimmer, or anything else), to the Berlin method (live rock and protein skimmer), the Jaubert method (live rock and plenum with no sump or protein skimmer), and all the way up to the most advanced high-tech systems that use some assortment of the following: multiple media reactors, protein skimmer, refugium, algae scrubber, calcium reactor, ozonizer, UV sterilizer, controllers, dosers, CO2 scrubber, and more. If this is already overwhelming, good, that means you are paying attention.

Why All the Methods?

All of these methods are variations around one important factor: nutrient export. Excess nutrients (nitrate and phosphate) in a reef system can be very damaging. They promote pest algaes which can completely take over the display, smother corals, and inhibit calcification. There are two primary natural methods of nutrient export and all these methods use one or the other: anaerobic denitrifying bacteria and photosynthesis via macroalgae.

Anaerobic denitrifying bacteria live where there is very little oxygen. Note that there is not a complete lack of oxygen, which is referred to as anoxic, because anoxic conditions allow for the development of toxic bacteria that produce hydrogen sulfide which can potentially kill your livestock (usually when it is accidentally disturbed). The best examples of anaerobic conditions are deep within the live rock and in deep sand beds and plenums. A plenum is an open space underneath the sand. The typical plenum is something along the lines of 3″ or so of open water underneath a platform of some sort that is holding up the sand and rock. This is generally considered better than a deep sand bed (which does not have any sort of open water space underneath it) because the open space allows for better flow and makes the method a little less likely to allow for toxic anoxic bacteria. Fortunately, there is very little mention of either of these methods anymore since both have a relatively high risk of also allowing for toxic, anoxic conditions (although you will still see deep sand beds brought up from time to time).

The photosynthesis method is definitely the better choice. Not only do you have no risk of anoxic conditions, but it also removes phosphate, not just nitrate as is the case with anaerobic denitrifying bacteria. Macroalgae function just like plants do, they carry out photosynthesis, which means removing CO2, nitrate, and phosphate while giving off oxygen.

how to set up a reef tankThe Natural Method

The method that I have developed over the years is nothing unique or magical, it is just what has proven to work best for me repeatedly and is the best starting point for new reefers. I call it the natural method because it is as natural as I am comfortable going without any unnecessary extra equipment or riskier methods. The basics of this method are:

  • Lots of Live Rock (1-3 pounds per gallon)
  • Sump
  • Strong Protein Skimmer
  • Strongly Lit Refugium
  • 10% Weekly Water Changes

That’s it. I don’t consider anything else to be an essential part of this method, but many systems may need a little more. The most likely addition will be an automatic top off (ATO). Many systems will also need GFO in a media reactor, at least at some point. Many may also develop to the point where it is easier to set up dosers rather than manually dosing every day. Don’t hesitate to add these features, automating these features is a great way to make reef-keeping more enjoyable and less work, just don’t think they are essential.

Biological Filtration

As long as you have enough live rock (1-3 pounds per gallon), you will have enough biological filtration. The nitrifying bacteria live all over the live rock and the strong flow of a reef tank allows for all the necessary biological filtration. You don’t need bioballs, porous ceramic media, filter blocks, or anything else.

Chemical Filtration

In most cases, you shouldn’t need any chemical filtration. If your water changes alone aren’t enough to keep the water clear, running carbon in a media reactor for 24 hours once per month may be beneficial. Some/most tanks need GFO in a media reactor at some point to help get phosphate under control. If this is the case though, you should re-examine your refugium light (discussed below).

Mechanical Filtration

I don’t use any mechanical media in my reef system at all. There isn’t a filter sock, foam block, pre-filter pad, or anything. I like to keep it all moving until natural filter feeders eat it. This is more natural, no maintenance for me, and I get to enjoy all the filter feeders without having to go out and buy products just to feed them. By using mechanical media, you are creating more work, trapping debris which will rot and release nutrients unless you are OCD about keeping them clean, and trap the food that filter feeders need which requires you to feed more if you want to have them (filter feeders being feather dusters, flame scallops, sponges, gorgonians, etc.).

Best macroalgae for refugiumsRefugium

The biggest challenge for most reef tanks is nutrient control. All tanks go through algae phases, but many are much worse due to excess nitrate and phosphate. Most of the advanced (and risky) features of reef systems revolve around nutrient export. GFO media reactors, deep sand beds, plenums, biopellet reactors, vodka dosing, Caulerpa spp. macroalgae, etc. are all methods of removing nitrate and/or phosphate. Almost all of these have significant risks (usually either overdosing which crashes the tank or allowing toxic anoxic bacteria). The safest, and best option if your tank needs a little help, is the GFO media reactor. There isn’t any risk with using it, but it is an extra expense and more maintenance.

The best macroalgae for the refugium is chaetomorpha, or chaeto for short (pronounced key-toe, not chee-toe or kay-toe). It grows rapidly and is safe to run 24/7. Caulerpa spp. run the risk of going sexual which can kill the whole system. Since there is no risk or downside to using chaeto, I can’t understand how anyone would risk their system by choosing Caulerpa over chaeto.

The refugium is probably the most important factor in getting this natural method to work. A refugium is nothing unique or innovative, but the way most people set them up really holds them back and makes their impact on the system minimal. Most people use hardware store clamp lights with compact fluorescent bulbs. Their chaeto just kind of maintains, it doesn’t grow like crazy. The nutrient export capabilities of the refugium are 100% dependent on and correlated with the growth rate of the chaeto. The growth rate of the chaeto is completely dependent on the lighting. Weak or ‘pretty good’ lights will produce weak or okay results. Even many refugium lights in the hobby are only a small step up from the weak hardware store lights, and not enough of a step to make a real difference.

For a refugium to effectively do its job and really suck the nutrients out of the system, the lighting has to be very strong. Macroalgae uses the same spectrum as plants, so the redder the better. The best lights I have found are LED grow lights made for hydroponics. They pump out a ton of light, with all pink bulbs, so they are very strong and the exact color needed for photosynthesis, making them the perfect chaeto grow light. This is the key to getting VERY fast chaeto growth, which really sucks the nitrate and phosphate out of the system. This alone can completely replace ALL those other nutrient export methods, almost all of which have risks. The refugium light on my current reef system is a 300 watt all pink LED hydroponic grow light I got on eBay for $60 shipped. It is too good (my tank runs too clean!).

People often think they need more than a refugium because they have one and still have too much nitrate and phosphate (Note: you have too much if you still have an algae problem, regardless of what the test kits say). In reality, they need to question their refugium. Just changing the light can completely change the entire system and avoid riskier nutrient control methods (and save a lot of time, hassle, and expense).

Flow in the refugium isn’t nearly as important as most people make it out to be. You will probably hear that slower flow is better, but this simply isn’t the case. Whether the water goes through quickly 10x per hour or slowly 2x per hour, it is getting cleaned. I have never heard a reefer say, “My refugium just isn’t do anything, there is too much flow.”

For more information, please read the article on How to Set Up a Refugium.

best natural reef tank methodsProtein Skimmer

The protein skimmer is the most unnatural aspect of this ‘natural’ method. All other aspects of filtration are achieved with completely natural methods. The protein skimmer is important because it removes food and waste before it is even broken down into ammonia. It is also a powerful tool in situations where something goes wrong. l in situations where something goes wrong. The best example is when something such as a large fish, clam, or anemone dies. The death of these types of animals is particularly bad for a tank because of how much waste is suddenly released into the system. When this occurs, a protein skimmer can make the difference between ‘What’s wrong with the tank?’ and ‘Holy crap, what happened?’ (a hurdle vs a crash).

The protein skimmer can be absolutely essential or unnecessary. Some systems really need them constantly pulling out all that waste. In other systems (or the same system later on as it and the keeper’s methods mature) they may not actually be needed at all. My current system doesn’t actually need the protein skimmer, and would actually benefit from the extra nutrients if I were to stop running it, but I just can’t stand the idea of risking everything if something large were to die, it isn’t worth losing it all.

Best Natural Reef Aquarium MethodsFeeding

A major part of nutrient control is nutrient input. If you are using RO/DI water there is only one input and that’s feeding. Unfortunately, this leads many people to cut down on how much they are feeding. This is only right if you were genuinely overfeeding. If not, then it can have serious consequences for your livestock. Fish eating well is vital for their long-term success. So even if the forced diet helps with algae control in the short term, it is very harmful long term. Well fed fish are also good for the corals and other invertebrates, since that is where they get their nutrition from. The natural method allows for proper feeding. You should never have to cut back on feeding just to try to keep algae under control. If anything, your system may run too clean.

natural reef aquarium methodWhat About an Algae Scrubber?

I haven’t used an algae scrubber yet, but I strongly believe they can be at least as effective as a refugium. They can require a tad more maintenance (when they need to be cleaned, they really need to be cleaned or they can’t do anything). I prefer methods that are a little more forgiving of forgetfulness/laziness/life happening, so I would lean toward a refugium, but I have no argument against an algae scrubber and I think of them as an ‘organized refugium’. The other issue is that there aren’t any manufactured algae scrubbers yet, so they are all DIY or custom jobs which either cost more or are more work for you. Tossing in some chaeto and turning on a light is just that much easier. But if you want to try an algae scrubber, do it. Just make sure it is large enough and has very strong lights.

Every system is different, and many take time to stabilize and reach a balance. Newer systems may need some help, most likely GFO in a media reactor. But don’t give up hope, as the tank matures and you iron out the wrinkles with the system and your routine, you will move closer and closer to a well-balanced, natural system. Don’t get discouraged. I think of aquariums like steering elephants, you can’t get them to completely change overnight, but gentle pressure in the right direction can get them going exactly the way you want them to.


Don’t get caught up in the overwhelming selection of equipment, gizmos, bells, whistles, and methods out there. Maybe you will need or benefit from a few of them down the road, but they certainly aren’t essential. Keep it simple.

Start with the natural method, and as you and the tank develop, mature, and advance, then you can focus on whatever is your limiting factor at that time. Start with the big issues first, and focus on one thing at a time.

Even I have been surprised at how well this method can run, and how reliably it maintains the ideal conditions for a reef. It is safer, less work, more natural, more diverse, and more stable.