Natural Nitrate Removal

Both fishes and corals produce waste, in fact, all the life in your marine reef does.

And that produces Nitrate. Like freshwater Nitrifying bacteria, their marine counterparts do the same thing; convert the Ammonia generated by fish urea into Nitrite, then Nitrate, which freshwater hobbyists dilute by regular partial water changes.

While mature live rock coupled with live sand can keep Nitrate quite low in smaller tanks with very few fishes, there are methods of eliminating it all together. Most test kits don’t have the resolution to detect low levels of Nitrate in marine tanks. But if one keeps reef fishes, believe me it’s there

First, Nitrate is an atom of Nitrogen and two of Oxygen. When those Oxygen atoms are removed, what you get is Nitrogen Gas, which all air-breathing life breaths (in fact, the the air we breath is 21 percent Oxygen, 70 percent Nitrogen).

There are two prevailing methods of naturally reducing Nitrate to zero constantly. They are deep sand beds and plenums.

What makes them work is the Nitrifying bacteria that exist in low Oxygen environments which are 2 ppm Oxygen down to .02 ppm.

What those bacteria do is take those two Oxygen atoms from the Nitrate for their own use, and the result is pure Nitrogen Gas.

Setting up a deep sand bed

A deep sand bed is what you think it is; a thick layer of sand. Three to four inches of sand capped by an inch of live sand. The sand is 2 to 3 mm.

With mature live rock and the live sand, soon the deep sand bed will be teeming with life. Copepods and other micro-crustaceans, miniscule brittle stars, tiny snails, and burrowing worms flourish, helping to keep the sand stirred, All that life produce tiny young, giving your corals live food of a proper size.

In a deep sand bed, the first two inches or so is where the bacteria that convert Nitrite to Nitrate live. Below them are the low Oxygen bacteria that convert Nitrate to Nitrogen gas.

One should provide Nassarius species snails since they burrow into the sand looking for detritus to consume. Their activity further helps in keeping the sand from compacting.

If you wish to see the proliferation of life in a deep sand bed, pick up a small piece of live rock. You’ll see dozens of kinds of benthic life under that rock.

The downside is all that sand takes up tank space. In a large tank that’s not a problem, but if your reef is a 55 gallon, four or five inches of sand may take up more tank room than you’re comfortable with.

Though there are species of reef fishes which must have a deep sand bed, the alternative for natural Nitrate removal is a plenum.


A plenum is simply a open space below the substrate. That’s the low Oxygen space where the bacteria convert Nitrate to Nitrogen gas.

One sets up a plenum with a box made of one-inch diameter PVC pipes of a size that nearly covers the bottom of the tank or sump. You silicone a Nylon screen to the box of PVC and place a two to three inch layer of sand that’s of a grain size too large to fall through the screen.

Like the above, those two to three inches are where the Nitrite to Nitrate bacteria live, and the open water beneath the plenum the low Oxygen bacteria reside, converting that Nitrate to Nitrogen Gas.

Personally, the sump/refugiums in my reef tanks are equipped with plenums. Since I keep relatively heavy reef fish populations, plenums are why my reefs never have any Nitrate, which has been verified by electronic meter.

There are, of course, commercial products designed for reactors that will remove Nitrate, but those must be refilled regularly, costing you money. A deep sand bed or plenum is set up and costs you nothing further.


9 thoughts on “Natural Nitrate Removal”

  1. nick

    Nitrate is No3 not No2. The air contains 78% nitrogen not 70%. If it was 70% nitrogen and 21% oxygen what’s the other 9%?.
    Why will life rock only remove nitrates in small tanks.
    A salifert test kit will test down to 0.2ppm!!!.
    A normal 2 inch sand bed will remove nitrates, along with good skimming. Yes a DSB will remove more nitrate but not a lot more!!!.
    You can never have zero nitrates. Corals need tiny amounts of nitrate to grow.
    As long as your nitrates are 1ppm or below, your S.P.S corals and tank will be fine.


    1. Cliff

      There’s lots of other gases in the air, such as carbon dioxide and carbon monoxide just to name a few. That would make up the other 9%

      You can have nitrates in trace amounts not measurable by most common test kits


  2. Peter Edwards

    For some 10 years I have had a tank and separate refugia with 3″ and 6″ sand respectively. I also have a plenum (under gravel filter beneath the 6″ sand). Also lots of live rock. My water chemistry is great except for nitrates I cannot get below 20ppm. Only have 5 fish plus inverts in total water vole of 250L. Tank water above sand well oxygenated. Really been costing me on water changes and at 65 its all getting a bit heavy! I wonder why I cannot get nitrates to a trace – any suggestions welcome.




    1. Cliff

      How have you been keeping the deep sand bed clean and free of trapped waste? All substrate needs to be maintained, or you will get a build up of waste that will result in nitrates being released into your water. In addition, when exposed to higher nitrate levels your rock will absorb nitrates to be latter released when the nitrate levels in the water drop.


    2. Andrew

      Check the water flow. Check for spots that are possibly open to flow through your substrate. Even “clumping”. Thats also a bit “too deep” and the top layer too high. You only need about 3-4” bottom layer of aragonite plus SCREENING between layers to prevent digging and natural “sagging” creating those holes and disturbing the anaerobic cycle.


  3. Candy

    Can you provide me with a little more information about setting up a plenum in a sump? My nitrates are high (even after a WC) and I’m trying to correct the problem. Thank you


  4. Candy

    Yes, it is a 75 gallon freshwater cichlid tank. A professional installed it and I do my own maintenance. The sump has 4 chambers. If you’re looking at the sump, the far right chamber houses the pump. The far left chamber is where the water comes in. That’s where I have my filter sock. The middle chamber is divided into two chambers, front and back. The front middle chamber holds nothing but water. The back middle chamber has a little white bobble thing in it (sorry, I’m not familiar with the term) and it also has a big black filter and a little black filter. I hope this makes sense. At one point, I had Nitrozorb, DeNitrate, carbon, filter sock and Purigen but my nitrates were still high. Now all I have is a filter sock and Purigen.

    Any help/advice you can give me would be appreciated. Thanks


    1. Cliff

      How high is your nitrate levels ? How often do you clean out the gunk from your sump ? Are you using any other filter media in your set-up (sump or otherwise) ?

      Fresh water needs a little different maintenance than a marine set-up


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