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Nutrient Control and Export:

Ways to Increase Water Quality and Eliminate Nuisance Algae in Marine Aquaria


By Scott Fellman

  MikeG's Caulerpa harvest of the day!

  As marine aquarists, we strive to provide our fishes and invertebrates with the highest possible water quality.  Collectively, we spend untold thousands of hours, and even larger amounts of money, working on ways to achieve this goal.  Countless products have been introduced to the market with the goal of creating optimum water conditions and eliminating the scourge of nuisance algae growth in our aquariums.  While there are a number of very useful products out there to get the job done, it is helpful to review the basic techniques used to accomplish nutrient control and export.  In this article, we will examine some simple techniques that you can use to control the accumulation of nutrients in your marine system, which, in turn, will lead to higher water quality and elimination of nuisance algae.


What Is “Nutrient Control And Export?” 

For the purposes of this article, “nutrient control” is the reduction of substances that can degrade water quality in captive marine systems. “Export” is the actual process of removal and elimination of these substances from the system.  Further, we’ll use the term “nutrient” throughout this article to identify any substance which can lead to degradation of water quality and the growth of undesirable nuisance algae.  In order to better understand how to control and eliminate these substances; let us look at how they get into our systems in the first place. 

Fish, invertebrates, and any other animals that we maintain in our captive marine systems produce nutrients through their metabolic processes, such as eating, respiration, and elimination of waste.  These metabolic substances are released into the water column, where they can accumulate to potentially toxic levels.  Fortunately, in healthy aquariums, as in nature, countless bacteria break these substances down into less toxic compounds. However, over time, many of these less toxic substances remain in the water, slowly but surely degrading the water quality, and leading to outbreaks of undesirable “nuisance” algae, unless the aquarist takes steps to control and eliminate them.  These substances include phosphate, nitrate, and silicate.  While all of these substances are present in healthy systems, excessive amounts of them can present long-term problems for the aquarist.  Let us look at some simple ways to reduce and eliminate excesses of nutrients in our marine aquaria. 


Nutrient Control and Export Mechanisms 

In this section, we will identify and discuss some simple techniques that you can use to help reduce and eliminate the accumulation of nutrients and get on the road to better water quality.  None of these techniques are revolutionary; most have been around as long as the aquarium hobby.  However, in our quest to achieve optimum water quality and control nuisance algae, we often overlook some of these basic techniques in our quest for “The Big Solution” to our problems.  

Source Water 

Water contains numerous substances which can affect the plants and animals that live within it in both positive and negative ways.  Of particular concern to us as hobbyists are substances such as nitrate, phosphate, and silicate, which, both individually and collectively contribute to lower water quality and outbreaks of nuisance algae.  When using source water, such as tap water, for “topping off” or mixing new water for our aquariums, we are often inadvertently fueling the growth of nuisance algae by providing them with a continuous source of basic nutrients. 

One of the best ways to eliminate nutrients from source water is to employ some form of pre-treatment, such as reverse osmosis and/or deionization.  RO/DI units are now available to the hobbyist in a wide variety of configurations and prices, and allow the hobbyist to produce virtually pure water at a very low cost.  Do keep in mind, however, that the membranes on these units do need to be maintained and/or replaced periodically if they are to continue to perform their function as a means of water purification. The frequency of RO/DI unit maintenance is largely dependent upon how much use the unit gets, and the amount of undesirable substances which these units are expected to remove from the water.  Many hobbyists who use RO/DI units seem to forget that they do need this maintenance, and it is often overlooked until water quality begins to decline and nuisance algae start to manifest themselves in the aquarium!  Do not neglect the maintenance of your water purification system- it is on the “front-line” of your battle against excessive nutrients! 

Mechanical Filtration Media 

A vast array of mechanical filtration media is available to the hobbyist, offering a wonderful means of removing particulate matter and detritus from the aquarium on a continuous basis.  These media range from the ubiquitous filter cartridges and ceramic “noodles” found in power filters and canister filters, to the “micron” filter bags, sponges, and polyester “prefilters” utilized in sumps and overflows.   These media are intended to remove gross particulate before it can accumulate elsewhere in the system.  However, many of these mechanical media are “victims of their own success,” if you will, and begin to accumulate large quantities of gross particulate and detritus, which slowly breaks down, and leads to the formation and accumulation of nitrate and phosphate. 

By regularly cleaning and replacing these mechanical media, it is possible for the hobbyist to remove large quantities of undesirable matter from the system before it begins to break down and degrade the aquarium’s water quality.  Many of these filter media need to be cleaned and/or replaced several times a week, or they can easily become a major contributor to nutrient accumulation in the system.  Some hobbyists have accumulated enough prefilters and filter bags to “rotate in” a new one several times a week, or even daily.  Trust me on this-if you replace your mechanical media on a frequent basis, you will see a very noticeable improvement in water quality and a measurable reduction in nitrate and phosphate accumulation within your system! 

Protein Skimming 

One of the very best means of nutrient control and export for captive marine systems is the continuous use of a protein skimmer.  It is arguably the best means of removing organic substances from the aquarium water.  An efficient, well-maintained skimmer can reduce the amount of organics present in the water before they break down and begin to accumulate.  There is little argument among aquarists as to the effectiveness of protein skimming for removing these compounds.  However, there are many different opinions as to which type of skimmer, and which model, is the “best.”  The review and comparison of  the relative merits of different skimmer designs is beyond the scope of this brief article; suffice to say that the inclusion of a protein skimmer in the marine system is, for most of us, and absolute necessity, and a key contributor to the maintenance of a successful aquarium! 

Of critical importance when using a skimmer is its placement within the system.  A skimmer should be placed at a location within the system where it will receive “raw,” unfiltered water, ideally from the surface of the aquarium.  This water has the highest concentration of organic materials and other substances that should be removed from the system.  The skimming should ideally take place before any other filtration occurs, with the possible exception of gross particulate removal.  This will ensure that the skimmer is receiving the largest amount of organics to work with. 

A skimmer should be adjusted so that it produces at least one to two cups of dark, yucky smelling stuff per week.   Stable, “dry” foam within the neck and collection cup of the skimmer is a sure sign that you’ve found the “sweet spot” within your skimmer’s operating parameters.  One thing that is a “constant” with protein skimmer use is the necessity for frequent maintenance of the skimmer itself.  The sludge that accumulates within the neck and collection cup of your skimmer actually inhibits the production of desired foam after several days, so for optimum performance, a skimmer should be cleaned at least once, possibly even twice, per week.  At the same time, inspect and/or clean venturis, injectors, and airstones which may be present in your skimmer.  You’ll be surprised at the increased efficiency that will result from regular skimmer maintenance! A well-maintained, properly set-up protein skimmer may be the best single contributor towards optimal water quality and nutrient control in a closed marine system. 

Water Changes 

Another one of the most basic aspects of aquarium husbandry (and one of the best means of achieving nutrient control and export!) is the performance of regular, modest water changes in your system.   In my opinion, smaller, more frequent water changes are preferred over larger, less frequent ones, and are much less labor-intensive.  Try changing as little as 5% of tank volume on a twice-weekly basis, and you’ll be astounded at the difference this will make in your system!  Fish will be livelier and more colorful, corals will open up like you’ve never seen them do before, and levels of dissolved organic substances, such as nitrate and phosphate, will decrease significantly.  Frequent water changes allow the aquarist to help dilute and reduce the concentration of waste products from the system before they begin to accumulate as nutrients.  This, in turn, will result in less potential for nuisance algae growth, and a more stable system. 

Remember to use high-quality source water when mixing up your saltwater for water changes.  Be consistent, methodical, and siphon out as much detritus as you can from the rockwork and other areas from the aquarium.   Frequent water changes also give the hobbyist the added advantage of being “in touch” with the system on a very regular basis, resulting in a better understanding of just what’s going on within his or her aquarium.  As the old hobby saying goes, “nothing good happens quickly in a marine system,” so the benefits of frequent water changes will begin to manifest themselves gradually-but they will become obvious after a brief period of time.  Give more frequent water changes a try! 


The best (and worst!) part of the marine aquarium hobby is choosing among the hundreds of available creatures in order to stock our aquariums.  With new corals, fishes, and other invertebrates hitting the market on a regular basis, we are constantly tempted to add new animals to our systems.  High tech protein skimmers, filters, and various “additives” often provide the hobbyist with a false sense of security, lulling us into believing that our system can “handle” an absurdly high biological load.  Despite our best intentions, the temptation to add “one more” fish, coral, or invertebrate can risk upsetting he delicate balance that occurs within our systems, and creates the potential for an over-crowded, unsanitary, and unsustainable aquarium.  It is important to “under crowd” our systems with animals, so that we may create a better life for our captive specimens. 

Over-crowded aquariums result in excess amounts of metabolic wastes, which will create seriously degraded water quality in little time.  An aquarium with a very high bioload   will offer little “margin for error” on the part of the aquarist.  The very real potential exists for the dreaded “crash” of the system,   a horrible situation where the toxic metabolites accumulate to rapidly for the biological filtration mechanisms to process and reduce them into relatively harmless substances.  Utilize common sense when stocking your aquarium, both in terms of the number and types of animals that you are attempting to keep.  The bottom line here, dear reader, is to resist that temptation to add more specimens to your system than it can handle! 

Foods and Feeding 

One of the easiest to control sources of excess nutrients in captive systems is food. Frozen and other prepared foods contain large quantities of phosphate and other organics that can seriously degrade the water quality in even the largest aquariums.  When feeding frozen foods, it is of utmost importance that you do not simply dump the food, frozen juice and all, directly into your aquarium.  The processing juices contain huge amounts of nutrients that may not be utilized by the life forms in your aquarium, and thus accumulate, creating optimal conditions for nuisance algae. 

Always thaw out frozen foods slowly in a container of water, then dump out the water, and feed the food with a toothpick or other small implement. Yes, this technique is a bit more tedious, but it will significantly reduce the amount of excess organics that enter the aquarium.  It is a basic tenant of aquarium keeping that you should only feed as much food as your fishes will consume in a reasonable length of time, and that uneaten food should be removed before it has a chance to decompose and affect water quality. 

When utilizing liquid foods, such as those developed for invertebrates, be sure to use a syringe or baster   to “target feed” the animals.  Some hobbyists actually remove animals such as Tubastrea, and even small clams, to a separate container to allow them to feed without fear of polluting the display tank.  The extra time it takes to do this can reward the diligent aquarist with much higher water quality, and less possibility of nuisance algae appearing in the display tank. 


Fortunately or unfortunately, we live in an era where technology makes it possible to produce all sorts of additives, “water conditioners”, trace elements, and other “extracts” which are supposed to somehow make keeping marine aquariums easier.  Manufacturers tout the effectiveness of their products in enhancing invertebrate growth, supplementing fishes’ diets, and helping to create “natural” conditions in our captive aquaria.  Some of these products are excellent, some not so good, and still others are outright junk.  When utilizing any additive, you need to ask yourself why you are using it!  If you are trying to “push” corals to grow faster, or make invertebrates grow larger, or even attempting to cultivate macroalgae, some thought must be put in as to what these products are doing to the overall water quality.  Some “additives” contain high quantities of sugars and other micronutrients which, if added without a lot of diligence, can turn an otherwise healthy, attractive aquarium into a virtual cesspool! 

There are many elements that can be replaced in captive systems by simply conducting regular water changes with quality source water and a good salt mix.  If you are adamant about using some additives (such as iodine, which is a commonly used additive), be sure to conduct water tests for that element, to make sure that you are not “overdosing” your system.  In fact, it is a good general rule of thumb to not add anything to your aquarium unless you understand exactly what it will do to the water quality, what benefit you expect from the product, and what the long-term implications are for its use. 

Use of Chemical Filtration Media 

An excellent means of nutrient control and export is to utilize some form of chemical filtration in your system.  There are many different products on the market that are formulated to remove everything from ammonia to phosphate, and many substances in between.  Use of commonly available, high quality activated carbon on a regular basis in your aquarium will help to reduce excess nutrients continuously.  Other fine products include specialized media, such as PolyFilter, which has an affinity for a wide variety of organics. 

Of particular importance when utilizing chemical filtration media for nutrient control is the regular replacement of these media.  In order to do the job expected of them, these products must be inspected and replaced as needed.  If used in accordance with the manufacturer’s   instructions, chemical filtration media can provide the aquarist with a safe, effective means of nutrient control and export.  It is my opinion that every aquarium should utilize some form of chemical filtration media on a regular basis. These media provide a convenient and cost-effective supplemental means of removing undesirable substances from the water with minimal effort on the part of the aquarist.   


Macroalgae play an important role in closed marine systems.  They utilize nutrients, such as nitrate and phosphate, which are found in abundance in most aquariums.  As they grow, they take up required nutrients from the water column.  

The use of macroalgae in marine aquariums is a matter of personal preference, but can provide the hobbyist with an affordable, natural means of exporting excess nutrients from the aquarium.  Many hobbyists grow and harvest “purposeful” macroalgae, such as Chaetomorpha, Gracilaria, Halimeda, and Caulerpa somewhere in their systems in order to assist in the control and export of excess nutrients.  By carefully cultivating and harvesting the macroalgae on a regular basis, you are literally removing excess nutrients from the aquarium.  The macroalgae may be grown either in a separate section of a sump, algal turf scrubber, or even a refugium, depending upon the hobbyist’s preferences. 

The degree of nutrient export provided by macroalgae is largely dependent upon the growth rate, density, and quantity of the macroalgae harvested.  Under optimal conditions, some species of macroalgae can achieve tremendous growth rates, providing the hobbyist with a wonderful means to export nutrients from his or her system. 

Deep Sand Beds 

Recent research by scientist and hobbyists alike has identified a superior means of nitrate reduction and nutrient export by utilizing a deep bed of fine aragonite sand in the aquarium proper, or in a specialized remote sump.   Deep sand beds (3 to 8 inches or more) have been proven to foster natural biological processes that serve to reduce nitrate and efficiently process organics in captive systems.  Some advocates of deep sand beds, such as Bob Goemans and Sam Gamble, suggest the construction and use of a plenum in conjunction with a sand bed, which provides significant nitrate reduction capabilities. Other authors and hobbyists advocate simply placing the suggested layer of sand directly on the aquarium bottom to construct their sand beds. 

Regardless of which approach to a deep sand bed the hobbyist utilizes, the benefits of a properly constructed, well-maintained deep sand bed are dramatic and impressive.  Deep sand beds are a valuable tool for the hobbyist to help maintain a more natural, biologically stable system, and provide a simple, efficient means of controlling and exporting nutrients from captive systems. 


One of the relatively new concepts in marine aquarium and reef keeping, but one that has caught on dramatically, is the use of a refugium attached to the main system.  As their name implies, refugia provide a protected place where delicate organisms can grow and reproduce, free from predation and harassment from other animals.  Many of the organisms which grow in refugia efficiently utilize and   process nutrients found in the water column as part of their natural growth processes.  Organisms such as feather duster worms, amphipods, copepods, small anemones, and even sponges, provide an amazing natural “filtration” service for the aquarist, and offer the added benefit of providing the system with a supplemental food source through production of plankton and other animals that find their way into the display aquarium.  The implementation of refugia into captive displays is almost a “sub-hobby” of its own, and should definitely be explored by hobbyists for its rich potential benefits. 

Other Natural Methods 

Some aquarists, such as Steve Tyree, have suggested the potential of sponges and sea squirts as part of multi-level “zonated” filtration for reef aquariums.  This concept is wide open for exploration by adventurous aquarists, and may offer an incredible means of nutrient control and export which has yet to be fully utilized within the hobby at this time.  Other authors, such as Anthony Calfo, point out that even so-called “pest” animals, such as the dreaded Aiptasia anemone, can be utilized in a sort of “scrubber” as another natural means of nutrient export. Still other hobbyists are experimenting with autotrophic animals, such as the soft coral Xenia, to perform the same function.  With a bit of experimentation, and a lot of persistence, the intrepid aquarist may discover entirely new means of nutrient control and export for captive systems.  There simply is no telling what types of creatures and methods may work in this capacity! 


I hope that this brief review of nutrient control and export methods has encouraged those of you who are struggling with high nitrate or phosphate levels, unstable water chemistry parameters, and nuisance algae growth to explore some of the methods that we touched on here.  None of them alone is the “one” answer to all of our problems.  However, by understanding what means of nutrient control and export are available, and how they can be implemented, you may just find the key to solving a problem that has caused you considerable grief!  One of the great things about our hobby is the ability of hobbyists at all levels to contribute to the general knowledge of marine aquarium keeping.  Perhaps you have found a better way to approach the problem of nutrient control and export, or simply have modified an existing approach to better suit your needs.  Either way, be sure to share your findings with others, so that the hobby, and most importantly, the animals which we keep, can benefit from your labor and research!



New Print and eBook on Amazon

Marine Aquarium Algae Control

by Robert (Bob) Fenner

Calfo, Anthony.   “Book of Coral Propagation,”  Reading Trees Publications, Monroeville, PA, ? 2001. 

Fenner, Robert.  “The Conscientious Marine Aquarist,”  Microcosm Ltd, Shelburne, Vermont, ? 1998. 

Tyree, Steve.  “The Porifera (Living Sponges), D.E. Publishing, Rancho Cucamonga, CA, ?1998. 

Goemans, Bob, Ph.D.  “Live Sand Secrets,” Marc Weiss Companies, Inc., Fort Lauderdale, FL, ?1999.

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