How To Control Nitrates In a Saltwater Aquarium

A new saltwater aquarium owner will quickly learn the benefits of an effective means of removing NO3 (nitrate) from the system, spurred on by the sudden appearance of unwanted algae during cycling. In this article we explore nitrates in a saltwater aquarium and what to do about them.  

This outbreak of algae can cover your rocks and sand, making your tank look unsightly.  The presence of cyanobacteria in a reef tank can also be attributed to high nitrate levels.

High levels in an already established aquarium are known to exacerbate the growth of zooxanthellae (a photosynthetic algae that lives in coral tissue), which in turn decreases coral growth and colour, turning them brown.

Understanding the basics of the nitrogen cycle and how it affects your system, will ultimately lead to your success in keeping nitrate levels under control.

The nitrogen cycle

The nitrogen cycle is a continual process that starts with the ‘cycling’ of a new tank.

When we refer to a new tank cycling we are referring to the beginnings of the nitrogen cycle which your system will rely on to maintain life in the tank.

A full blown explanation of the nitrogen cycle can become very technical, and quite simply it isn’t entirely necessary to understand every aspect.  

Below is a simplistic breakdown that will help you understand what you can do to control nitrate in your tank.

Ammonia (NH3):

When you are cycling a new tank for the first time, NH3 will be the first compound that a dedicated test kit will measure in the nitrogen cycle. The reason for this is that any organism ‘die-off’ will have decayed and released NH3.

The first of the nitrifying bacteria to exist in a marine system are ammonia consuming bacteria which convert NH3 into Nitrite (NO2).

This does not mean that you are now done with NH3. Your system will constantly be creating lower undetectable levels of NH3 which will continuously be consumed and converted into NO2 by nitrifying bacteria.

Nitrite (NO2):

Having consumed and converted NH3 into NO2, there is another type of nitrifying bacteria will consume the NO2 and convert it into Nitrate (NO3). When cycling a new tank this is the second compound a dedicated test kit will measure, as confirmation that the nitrogen cycle is in process.

NO2 will constantly be created at lower undetectable levels in your system, consumed and converted into NO3.

Nitrate (NO3):

When you have detectable levels of NO3 in your new system, measured with a dedicated test kit, you know that all nitrifying bacteria are present and doing what they should.

Fish and coral should not be added until there are no detectable levels of NH3 or NO2.

When these are no longer detected, you know that your system has enough nitrifying bacteria to deal with the current bio load.

Aerobic bacteria (nitrifying bacteria as above) live on the outer layers of live rock. Anaerobic bacteria inhabit the inner oxygen poor centres of live rock, and it is these bacteria that convert nitrate into nitrogen, completing the cycle.

Common causes of nitrates

An increase of nitrates in a saltwater aquarium can be caused by any one, or a combination of, the following:

New tank cycle:

The cycle is kicked off by the addition of live rock. During transport (out of water) before it gets to your tank some organisms living on the rock will die. These dead and decaying organisms begin the nitrogen cycle.

Fish food:

There are many options of fish food available from flakes, to pellets to frozen mysis shrimp. Flakes and pellets contain organic plant matter and fish meal, while frozen fish food contains dead brine shrimp, mysis shrimp, red plankton, lobster eggs, krill and many more. 

Uneaten food will break down and decay in your system. This is why it is important to feed your fish correctly, preventing over-feeding.

Coral food:

There are many effective coral foods on the market which are ground down to a miniscule size that will allow even sps corals to consume them. However, unlike fish food which can be eaten by the fish in mere seconds during feeding, coral food works by floating around the system giving coral the chance to snag some from the water column. This can lead to uneaten food in your system.

In addition, amino acids are often added to a system for the benefit of the coral. These do convert into nitrates too.

Uneaten food will break down and decay in your system. This is why it is important to feed your fish correctly, preventing over-feeding.

Fish waste:

What goes in must come out, and in the case of fish it goes directly back into the water. Without the correct flow and water circulation it too can settle in the tank.

Death of livestock:

Unfortunately this can happen from time to time, losing a fish or invertebrate. If you have an effective clean up crew they will deal with a smaller fish over night. It will simply just disappear. 

However, leaving a dead fish or crab, or snail, in your system will allow it to decompose and cause a nitrate spike.


This refers to muck in your tank from all of the above.

How to control nitrates

1. Do not overfeed:

The main contributor of nitrate in any tank is excessive feeding. This can lead to uneaten food decaying in the system, and if you are over feeding on a daily basis the situation is compounded day on day.

What you should ideally be aiming for is all food to be eaten in a 15 to 20 second period at each feeding. This will ensure that most if not all of the food is plucked directly out of the water by the fish, not allowing it or giving it the time to settle in the tank.

Some fish only require a feeding once a day, while others like Anthias need more regular feeds. Ensure that fish which eat regularly have the days portion shared out equally between feedings. Don’t give in to feeding more than is needed.

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2. Do not overstock your tank:

Any tank will have a limitation on fish it can sustainably hold. The more fish you have in a tank, the more the bioload will be. The higher the bioload is, the harder the bacteria which control nitrates will have to work. This has the potential to lead to excessive nitrate levels.

By stocking your tank correctly, you will be ensuring that nitrate levels will remain within a sustainable level, making control easier.

3. Remove dead fish and/or invertebrates immediately:

You may have a very efficient ‘clean up crew’ consisting of snails, hermit crabs and not forgetting the much maligned bristleworm. Therefore the death of a fish may go completely unnoticed until you realise it is missing. 

However, should you see a dead fish, crab or snail in your tank you should remove it as soon as possible.  Giving it the chance to decay in your system will definitely raise your nitrate levels.

I may just point out that invertebrates do moult their exoskeletons as they grow.  Should you find what looks like a dead shrimp or crab, don’t panic immediately!  Like the shrimp below, it may have just moulted.

If you do find a moult in your tank, it is not entirely necessary to remove it as it contains nothing more than exoskeleton which does not decompose, but disintegrates over time instead.

By stocking your tank correctly, with invertebrates, you will be ensuring that nitrate levels will remain within a sustainable level, making control easier.  (Not sure how many snails you might need? Take a look at this article.)  

4. Clean mechanical media, if using:

Mechanical filtering media are often referred to as ‘nitrate factories’. They encompass any traditional media normally associated with freshwater aquariums.  Bio balls, fine or coarse sponges and even filter floss, have the potential to trap detritus (which is what they are made to do in freshwater aquariums) and raise nitrate levels.

Bioballs have no place in saltwater aquariums any longer. They were in primary use before it was realised that live rock acts as biological filtration.  With live rock forming the basis of your filtration, most mechanical media has become redundant.

Biological media (bio media) on the other hand can be beneficial to a saltwater aquarium.  To read more about it, you can read this article. 

Sponges are still in use to ‘polish’ the water and keep particles from floating around in it, as is filter floss, but the user is aware that these need to be cleaned or replaced every 2 to 3 days to discourage the increase in nitrates.

Filter socks are also widely used in marine tanks, and again they do serve the purpose of catching particles in the water column, but left too long and they will become traps for detritus leading to … you guessed it … an increase in nitrates.

How to reduce high nitrate levels

Luckily there are a few ways to reduce nitrates in a saltwater aquarium.  You can do what is easiest for you and what fits in with your schedule.

1. Do water changes

This is the staple of nitrate control. To make a water change as efficient as possible it is advisable to blow off the live rock with a turkey baster first. This will blast any settled detritus into the water column which can then be removed by use of a syphon. If the syphon is passed over the top of the sand it has the potential to lift detritus from the sand bed too.

Syphoning of the sand bed is a debatable subject, but if you consider that the sand is alive with microorganisms dealing with detritus, it becomes counterproductive to sift through the sand.

The average water change is approximately 10% per week or fortnight, but this can range from 5% to 33% depending on the results you are trying to achieve. For instance, if you want nitrate to be lowered from 10ppm to 8ppm in a 100L system, you will be required to do a 20% water change to achieve that result.

It is also worth mentioning here that there is a growing popularity to run systems with no water changes.  This is due to the owners feeling that water changes disrupt the stability of their systems, specifically in sps dominant tanks where the coral is susceptible to sudden change.  Many owners of sps and to a lesser degree lps, find that the benefits of water changing no longer apply to their system as the elements and trace elements being replaced are insufficient to their needs.

2. Add biological filtration media (bio media)

Boxtech bio media and Siporax can be used as an effective form of nitrate control in a sump, rear filtering system or external filters. It should not be confused with similar looking ceramic media. They act in much the same way as live rock, by creating an environment for nitrifying and denitrifying bacteria to flourish, while at the same time those that break down organic substances. Dying bacteria therefore do not block the pores of the media as would happen in ceramic media.

They can be used as the main filter media on fish only systems where no live rock is in use, or to supplement your existing live rock which increases the bacteria needed to deal with the nitrogen cycle.

Read more about Bio Media here.

3. Treat with Red Sea NO3:PO4:X (more commonly known as NOPOX)

NOPOX is another well known method of nitrate (and phosphate) control. Essentially it is a controlled daily dose of a ‘unique complex of carbons’ that are utilised by bacteria in a marine system which in turn break down nitrate and phosphate.

NOPOX is marketed as a complete solution for control of nutrients, therefore should not be used in conjunction with any other forms of nitrate or phosphate removal.

NOPOX is used in close association with tested nitrate and phosphate levels, maintaining a healthy nutrient balance, and a capable skimmer. Dosing without testing your nitrate and phosphate levels regularly can result in a tank crash.

Red Sea NO3:PO4-X, Nitrate and Phosphate Reducer, 1 Liter

4. Add a bio reactor

Bio reactors, like other reactors, are driven by a pump to rapidly circulate water within them. The difference however is the media they circulate. Bio reactors often get confused with a mechanical filtration reactors, but what sets them apart is the ability of nitrifying bacteria to live on the media known as bio pearls or bio pellets. 

As the bio pearls are an ideal living environment for the bacteria, they become concentrated within the reactor, extracting nitrate from the water being pumped through.

Bio reactors are unfortunately only suited to sumped systems.  And when running a reactor, it is extremely important to have a skimmer capable of handling the effluent created by the bacteria.

5. Consider adding a refugium, if possible:

The purpose of a refugium is multifaceted.

Primarily it is a part of the sump utilised to grow macroalgae under a grow lamp. The macroalgae thrives on nutrients in the system and will utilise nitrates in a saltwater aquarium to grow, thereby reducing them. The most common macroalgaes in use are cheatmorpha and caulerpa, both of which are easy enough to come by from sites such as ebay or dedicated forums or groups such as Facebook as well as other local aquarium owners.  

These macroalgaes can be free floating, or in the case of caulerpa, planted into a substrate.  You can see the pros and cons of two of the most popular here.  

A refugium can become a harbourage for amphipods and copepods to breed and proliferate, and eventually become free live food to your fish.

Macroalgae also provide a means of oxygenating the water. As with any plant, they will use the CO2 in the environment and release oxygen back into the water.

6. Vodka Dosing - WITH CAUTION!

Vodka dosing can also be used very effectively to control both nitrates and phosphates. Vodka dosing falls under the umbrella of carbon dosing. Carbon dosing can also use sugar or vinegar.

Adding organic carbons to your system in a controlled dosage increases the bacteria responsible for nutrient control.

As above with NOPOX, a very capable skimmer is required and close monitoring of nutrients is essential.

Vodka doing must be extremely closely monitored as it does have the potential to crash the system by bottoming out both nitrate and phosphate.

What if I have no nitrates?

0 nitrates?  Invariably, every saltwater aquarium needs a form of nitrate control and export (removal from the system), however it is also important to know that nitrates is a food source for corals.  

For this reason it is never good to have no nitrates.  In order to keep nitrate in your system it may be required to dose nitrates.

Unfortunately, not only does a lack in nitrate in a system have the potential to cause the death of corals, it can also lead to the beginnings of an invasive algae known as dinoflagellates.  Having suffered from dino personally, I would urge any reef keeper to maintain nitrates between 2ppm and 5ppm to avoid a crash.


There is no magical overnight cure for excessive nitrates in a saltwater aquarium.

It is without a doubt, one of the most difficult aspects of reef keeping to overcome. What works in one tank, may not work in another.

Removal of nitrates has to be approached methodically by establishing and removing or minimising the source. Once done, then put measures in place that will successfully lower existing levels and if that has been achieved successfully, maintain those levels in the same manner.

It can take four or more months to see the result of a method you have put in place working well.

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I am the owner of The Salty Side.
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How to control nitrates in a saltwater aquarium