How to Lower Nitrates in a Reef Tank

Nitrates are a big problem for reef tanks. Unchecked, they’ll create a massive algae bloom and can harm the health of your fish. As the most common pollutant in tanks, they’re often kept in check by just running a balanced system but that’s not always the case.

If you’re ready to take action and learn how to lower nitrates in a reef tank then read on!

reef tank


What You Need

You may or may not have some of the things on the following list already, but you should have all in use to keep nitrates down to the acceptable range of .25ppm-5ppm. You can always hold some in reserve if you reach your goal first and may run into problems later, but it’s best to have all of them functioning at once to control your nitrate levels.

  • Test Kit- To test nitrates and ensure you’re in the right range.
  • Protein Skimmer- A useful measure to help keep pollutants down in your tank. Most reef tanks should have one already.
  • Refugium- Either a pre-built model or plumbing in one made from scratch. The macroalgae will help reduce nitrates in the water column.
  • New Filter Media- Old media can increase nitrates, but don’t throw out your bio-filtration media!
  • Pellet Reactor- A simple device that can help reduce nitrates by creating a spot for more bacteria to grow in the tank’s water.

These items will all help along the way, but you also need to make sure that what you’re running is up to snuff already. We’ll handle that in the first step below.

So, get your things together or order them and we’ll start with the basics and keep going until your nitrates are in a good range.

1. Check Existing Equipment

You’ll want to go over all of your existing equipment before you start.

That includes anything that touches the water column, from filters to powerheads to piping. Check thoroughly for places that can trap debris to rot and clear out anything that’s been clogged.

Filter socks are a great example of things that can cause problems but might be overlooked. Remember to clean them on a regular basis or they may catch matter that rots in the tank, creating more nitrates.

You should also make sure your filter or filters are fully running. It’s a bit harder to tell with canisters, but HOBs should be returning an unbroken stream the width of the output. Canisters often make noise when things are slowing down, but you may also be able to tell by putting your hand by the output to see if it’s weaker than normal.

You should replace your media in line with the manufacturer’s recommendations in most cases but leave the bio-media alone. While activated carbon and sponges can create places for bacteria they can also contribute to nitrate levels if they get too dirty.

Check all powerheads, skimmers, and other equipment for proper functions at this time.

Before you begin, note which pieces of equipment may need servicing. It’s always best to handle things in tank water, so you can clean and maintain any equipment during the next step.

2. Water Change

If you haven’t been doing water changes on a weekly basis… well, we’ve probably found the source of your problem already. Water changes are the number one way to help keep nitrates under control in a reef tank.

I prefer to change the water at a rate of 25% every week, but you can go lower. Salt can get expensive for large tanks and it can be a serious chore.

A schedule of 15-20% once per week and a 25% change once per month is a healthy way to go.

If your nitrates have peeked over 10ppm, then you may need to commit to doing more frequent water changes or increase the volume for the time being. A 50% water change done once can help drive nitrate levels to a manageable level for the other methods that we’ll be using.

The important thing is to have a serious schedule for water changes and stick with it. This is the best way of removing unwanted nitrate from the water column by far, but it’s also the most labor-intensive.

3. Use a Protein Skimmer

Protein skimmers are essential for the health of marine aquariums, removing detritus, proteins, and other debris from your water. They consist of a small chamber that has an air pump running into it and an upper chamber that collects the foam generated during the aeration.

You then collect the foam and dispose of it, along with the trapped organic compounds contained within it.

They’re relatively simple to setup at home if you don’t want a commercial one. I’m really not sure how much money you’d save compared to buying a cheap one, but if you already have the materials it’s just a few hours of work.

Protein skimmers are pretty foolproof for the most part. As long as the air stone is working and the water level is high enough for foam removal you’re good to go.

The point is that if you’re not using a protein skimmer on your reef tank then you should. They help with nitrate removal as well, but they should be a designated part of any marine tank.

4. Add a Refugium

The main problem with nitrates is that they cause algae growth. With a refugium, we use some macroalgae, a light, and a bit of plumbing wizardry to help strip the nitrate out of the water. 

Ideally, the macroalgae will out-compete the smaller algae in the tank. You see a similar effect in planted tanks, where the answer to brown algae is often just to add even more plants to the tank.

Ideally, a refugium will be about 10% of the main tank’s size. Refugiums are sometimes used as a sump, but they’re generally not large enough and a dedicated sump doesn’t mean you shouldn’t also run a refugium.

The hardest part of setting one up, in my experience, is just finding enough space for it to remain hidden. The plumbing is fairly simple and only requires two tubes and two powerheads to complete. One pumping from the tank and the other pumping back in.

Refugiums range from simple, bare tanks that just host a bit of macroalgae to hosting their own complex system. The latter is more efficient for removing nitrates and usually consists of live sand, live rock, and small invertebrate scavengers in addition to the macroalgae.

Often, a refugium will also host a protein skimmer, reaction chambers, and other unsightly equipment if there isn’t a separate sump for the tank.

Commercial refugiums, with everything required, are great but they’re also very expensive. For that reason, many aquarists will simply spend the time to make their own.

5. Pellet Reactor

Pellet reactors hold a bunch of bio-media that contains bacteria. Water is consistently pumped through them, usually by means of an air pump. The reactor is usually only half full of media, which makes it tumble as the water passes through the chamber.

They’re a relatively cheap item overall. Just a few bits of plastic.

The media is the key here. As it tumbles and floats it collects more and more bacteria, which then process nitrate at a higher rate. They also seem to increase the efficiency of protein skimmers, which is a nice bonus.

As a general rule, these pellet reactors only need to be used on tanks with a very high bioload. If you have a proper refugium and protein skimmer that can’t keep up, then you may want to add one to your setup.

The ideal place to put your reactor is on the intake for your protein skimmer.

What happens is that as the media within the pellet reactor tumbles, bacteria are feeding on it. These are knocked off the pellets during the tumbling motion. If you have the reactor set up before the protein skimmer, it will remove some of these bacteria.

That might sound like a bad thing, especially considering all we do to maintain healthy populations of bacteria in our aquariums. Instead, it works out to a net nitrate loss in the water. The bacteria often die in the actual aquarium, which makes it much harder to come out with a net result of lowered nitrates.

Bottom line is that a pellet reactor is the last line of nitrate lowering before we get to more drastic measures.

6. Reduce the Bioload by Removing Fauna

If you’re still not able to keep nitrates at an acceptable level with the above measures you only have two real options.

The easier one? Remove some fish.

Chances are the tank is massively overstocked if you’re still running nitrates despite the previous measures. This isn’t always readily apparent at first glance for newbies, especially if they were taught the 1” to 1-gallon rule without any further instruction.

Removing fish will lower nitrates. Less waste is produced, so there’s less waste in the column. It’s foolproof.

Fish that are messy eaters or known polluters can require a ton of space compared to their size. Check carefully through all known information on the fish you’re willing to remove and place them in another tank.

If you don’t have a secondary tank suitable, then you can usually take them to your LFS for some credit.

Managing the bioload in your tanks is important, but the only way to lower it is to remove creatures from the tank. It’s not a lot of fun to pull your fish out of the tank, but it may be necessary.

7. Build a Sump or Expand Your Existing One

If you don’t want to remove any fauna, this may be your only option when all of the equipment mentioned so far is in place.

A sump is a secondary tank that’s plumbed into the main tank. They’re the usual place for equipment like protein skimmers and pellet reactors. The majority of reef tanks will have one, but if you don’t then it’s a great idea.

Sumps help keep water quality in check by increasing the total volume of available water in the system. In general, a sump should be at least 25% of the volume of the main tank, but more is better.

Plumbing a sump is simple if you know any plumbing at all, but it requires that you have either an overfill or running piping and tubes into the tank. Often the intake/output is placed in tubes run through drilled aquarium glass.

Drilling glass is difficult, risky, and time-consuming. If you’ve done it before you’ll be fine, but I wouldn’t want to learn how to drill glass while working on an aquarium I intended to keep. You have to keep track of heat and pressure, all while keeping the drilled piece wet.

But, at this point, we’re looking at drastic solutions. Set up a sump however you can or try the next step.

If you have an existing sump plumbed into the tank then it may need to be expanded. A bigger sump is better in all ways, size is the real limiting factor. I’ve run heavily stocked 10-gallon tanks with a 30-gallon sump before, the increased water volume meant a crystal clear, low-nitrate tank while I maintained a borderline hazardous stocking level.

A bigger sump will eventually fix the problem, it’s just a matter of whether or not you run out of space before the tank’s nitrates become acceptable. 

Low Nitrates, Clear Tank

Learning how to lower nitrates in a reef tank isn’t nearly as hard as you’d think. It’s just a matter of learning the equipment available for a reef keeper and then using it to the best of your ability. In most cases you won’t even have to consider the last two steps, so start from the beginning!

So that’s the general outline for a plan to keep nitrate in check. What do you plan on doing with your new, sparkling clean, algae-free tank?