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What Causes High Nitrate in a Freshwater Aquarium?

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Everything else could be going well in your fish tank until the nitrate levels shoot up, after which things take a nosedive.

Knowing how to quickly get the high nitrates down and what caused the spike in an aquarium will allow you to correct the absurd levels your test kit is showing.

Timely removal of the built-up nitrate is essential, especially in smaller tanks, such as the ones Betta fish and Goldfish are often kept in.

This is because smaller tanks get polluted way faster than larger ones, leading to violent fluctuations of the water parameters, including Nitrate.

So without much ado, let’s find out how to lower the high nitrate levels in a freshwater aquarium and fix the issue.

Before we start, let’s take a moment to understand the concept of the nitrogen cycle.

  1. Fish in the aquarium will eat and constantly produce waste.
  2. Another source of waste is the uneaten food particles that slowly decompose on the tank’s bottom.
  3. Dead plant leaves and other organic matter eventually end up decomposing into Nitrate.
All this waste degrades to ammonia (NH3), which jumpstarts the nitrogen cycle.

A colony of bacteria called Nitrosomonas then reduces the ammonia by converting it into nitrites (NO2-).

The bacteria feed on ammonia and then release nitrites as a by-product. The rate of conversion depends on the size of the bacterial colony.

Nitrites are highly toxic to freshwater fish and in fact have the potential to kill, just as fast as ammonia.

Fortunately, other bacteria called Nitrobacter are on standby ready to render the nitrites by converting them into nitrate (NO3-).

The nitrogen cycle is then complete since nitrate remains inside the aquarium until you intervene to get rid of them.

Nitrate may be less harmful to fish than nitrite or ammonia but only in small doses and in the short run.

If you let them accumulate and remain in the aquarium water at high levels, they may slowly become a health hazard to your pet fish.

Even levels of 20 ppm will sooner or later cause an intoxication for aquarium fish.

What causes high Nitrate levels in aquarium water?

When there’s a high accumulation of nitrate in the aquarium it’s important to react fast as fish mortalities could soon take place.

The NO3– ion does not get converted to anything in a home setting and remains in the system.

In order to prevent an aquarium crash you’ll need to understand the reason behind the accumulation.

Contrary to popular belief, a level of 20 ppm of nitrate could become toxic to freshwater fish and invertebrates over time. Keeping the levels of Nitrate under 10 ppm, and ideally under 5, will result in healthier fry, no stunted growth, extended lifespan of the fish, and no algae outbreaks.

The Nitrate levels in an aquarium may remain high due to excessive water pollution. Repetitive overfeeding and insufficient filter media maintenance are often the main contributors to the pollution of the water.

That being said, I will break down each cause behind the high nitrate levels that built up in your fish tank:

  • Polluted filter media. Sometimes the cause for high nitrate is old filter media, clogged with gunk.

    It’s important to rinse said media in non-chlorinated water every once in a while to prevent the build-up of Nitrate ions (NO3-) to levels that may be harmful to the fish.

  • Lack of live aquatic plants. Aside from providing a natural setting, live aquatic plants use up excess nitrate in the water as a source of food for growth.

    This, in turn, provides indirect benefits to the fish, as the lower levels reduce osmotic stress, while the plants provide hideouts.

    Having plants in the aquarium is one of the very few natural methods for passive nitrate removal.

    It should be noted that having too few live plants in the tank can be more of a contributor than a solution to nitrate build-up.

    When there are only 1 to 2 aquatic plants and you forget to prune them regularly the decaying plant matter will outweigh the benefits of nitrate consumption.

  • An overstocked aquarium. The reason why the nitrate levels may remain elevated could be overstocking the tank with more inhabitants than it can handle.

    The organic waste piles up fast and it becomes a challenge to physically remove the persistent Nitrate on time if the fish tank is not spacious enough for its livestock.

  • Overfeeding the fish. Overfeeding is one of the main reasons behind increased waste production and uneaten leftovers leading to higher nitrate levels building up in an aquarium.

    A fish might overeat in its natural habitat and get away with it but in a limited space and a closed system, things can get out of hand at an alarming pace.

    Feeding once every other day, and no more than your fish can eat is a good rule of thumb here.

  • Poor tank cleaning and maintenance. The smaller the tank the more diligent you need to be with the cleaning.

    A poor gravel vacuuming schedule can very well be the reason why the nitrate levels in your tank keep getting high.

    Regular cleaning alongside filter media rinsing can help in keeping good water quality and aquarium hygiene.

  • Neglected water changing schedule. Changing the aquarium water on a well-thought schedule goes a long way in keeping nitrate in check.

    Dilution is often the solution to pollution.

  • Nitrate-rich tap water used for water changes. Fertilizer runoff and other wastewater sometimes leach nitrogen in tap water supplies.

    Though water facilities do their best to remove contaminants, some NO3– ions may remain unfiltered.

    The EPA (the United States Environmental Protection Agency) has set a limit to what tap water can contain and in the US the legal content of Nitrate could be up to 44 ppm.

    However, in the context of keeping freshwater fish, introducing even 5 ppm of nitrate with water changes should not be overlooked.

    In that case, a healthy soure for tank water would be remineralized, purified water.

How to fix the elevated Nitrate levels and lower them?

Lowering the nitrate levels in the aquarium should be a gradual process in order to avoid shocking your pet fish further.

Removing such contaminants too fast may cause stress and sometimes death to fish because of the sudden difference in ion concentration in the water.

This is sometimes expressed as buoyancy issues because the fish need time to adjust and regulate their body fluids.

The organs of the affected fish then swell, putting pressure on its swim bladder, which is responsible for the balance during swimming.

After the levels are under control you need to seek ways to keep them that way to avoid further health complications in the fish.

That being said, to fix the high nitrate levels in your aquarium water follow these exact steps:

1. Change 5% to 10% of aquarium water every hour.

To lower excess levels of nitrate, doing a water change is necessary to physically get rid of the contamination in the quickest possible way.

First, you’ll need to perform a water test, using a liquid test kit to establish the severity of the issue.

Test strips are not reliable when it comes to establishing accurate water parameters.

Aim to bring the nitrate level below 20 ppm.

In the case where the nitrate content is very high, however, the removal should be gradual.

Do not remove more than 50 ppm of nitrate per day, as that’s as much as freshwater fish could tolerate before getting stressed.

The percentage of water volume you interchange will correspond to the percentage of nitrate being removed from the system.

If you exchange 25% of the water in the tank, then that would correspond to removing 25% of the Nitrate, given that your tap water is completely free of NO3– ions.

To safely reduce the nitrate levels, perform a couple of 5% water changes every hour or so until you reach the daily limit or the desired effect.

If you need to remove more than 50 ppm of Nitrate in total, then you can safely resume the water changes on the next day.

Frequent partial water changes are a quick fix and should be your first resort if your fish tank experiences extremely high nitrate levels.

However, the effect will be temporary, as it is a mere emergency response.

For long-term solutions, check the methods listed below.

2. Introduce floating aquatic plants to the system.

Have you wondered why high nitrate levels usually trigger an algae outbreak in an aquarium?

Plants absorb nitrate, which they then utilize to make energy for growth. In other words, nitrate is essentially a plant food.

Introducing high nitrate-absorbing plants to an aquarium considerably helps to reduce the nitrates in the system. Floating aquatic plants are one of the best candidates for this because they grow really fast and require lots of nutrients along the way.

Another reason I’m recommending floaters is that they have easy access to atmospheric CO2.

The more CO2 a plant can get, the better and easier it will utilize nitrate from the water. Therefore, a long-term fix for a high nitrate problem in a freshwater aquarium is to make good use of floating aquatic plants.

A good list of floating freshwater plants for passive nitrate reduction would be:

  • Water spangles
  • Hornwort (can be both planted or floating, but I recommend letting it float for better efficiency)
  • Water sprite
  • Amazon frogbit
  • Giant duckweed

Note that this method could even reduce the need for water changes.

3. Interchange tap water with RO water.

Sometimes tap water has a high concentration of nitrate, to begin with.

In that case, even after you do a water change, you introduce the contaminant back in the system, which defeats the purpose.

In that case, switching to water purified by reverse osmosis (RO) may be a very efficient long-term fix.

The reverse osmosis process removes most impurities, including higher concentrations of nitrate, which can make the difference if you struggle to get them down by using water from the tap.

You can likely buy RO water in your local fish store on a “per gallon” pricing model.

However, in the long run, it’s wiser to invest in your own RO/DI filtration system in order to save money.

There are a couple of good RO DI systems specifically designed for aquarium use out there.

The RO systems listed in the link above are suited towards use for saltwater reef tanks but bear in mind that corals are the most sensitive aquarium pet when it comes to water purity. For this reason, you can bet that these RO DI systems will work wonders for purifying the exchange water for less-demanding freshwater fish tanks.

I can directly point you to this inexpensive one which I’m personally pleased with, but you can do your own research on the matter.

The first step here is to check the nitrate concentration in your tap water.

If it is alarmingly high, you should opt for an RO filtering system to correct the issue with high nitrate levels in the long run.

You can call your authorities and ask for a free report of the water quality in your region or you can simply test it with a liquid test kit such as the API Master test kit.

4. Set up a refugium with lava rock and grow algae in it.

A refugium is another tank linked to your main one via tubes and a pump that circulates water through both.

Lava Rock is porous enough to create anaerobic conditions in its pockets for de-nitrifying bacteria to form a small colony.

Unlike the beneficial bacteria that are aerobic, these de-nitrifying bacteria are anaerobic which means that they thrive in poorly oxygenated conditions.

De-nitrifiers convert Nitrate into harmless Nitrogen molecules.

Lava rock can also be a bit too sharp to be put in an aquarium with long-finned fish, hence my recommendation to put it in a refugium and link both tanks.

In addition to this, installing an LED light, over the refugium will encourage the growth of algae.

Aquatic algae are really good at sucking up excessive nitrate.

With a refugium, you keep both algae and the lava rock away from your display tank, while exploiting their benefits.

The upfront cost of setting up such a system is a bit higher, compared to the other methods listed here but the long-term success will speak for itself.

Setting up a refugium where the de-nitrifying bacteria can convert nitrate into Nitrogen is a really efficient tactic to keep it at safe levels in an aquarium.

It requires extra space, so only venture into it if you can afford to have a place for the refugium.

Bear in mind that with everything in order, this setup has the potential to almost completely remove the nitrates from a freshwater aquarium, which in turn eliminates the need for frequent water changes.

Note #1: For de-nitrifying bacteria to form a stable colony the flow rate in the refugium needs to be really low.

Ideally, you’ll want around 30 to 40 GPH (gallons per hour) of the flow rate.

Finding such a small pump can be a bit of a challenge but a small Hydrofarm one should do the job.

You can also put some decorations near the intake in your display tank to additionally reduce the flow rate if needed.

Note #2: The establishment of de-nitrifiers takes up to 6 months, so this is not a good method for the impatient or people who are not in the hobby for the long run.

5. Reduce feeding to once every other day.

A common cause for nitrate levels that are alarmingly high is overfeeding your fish.

Some well-meaning but misguided aquarists tend to feed their aquatic pets more than twice a day.

Instead, set a timetable to guide you.

For instance, you can reduce feeding to once every other day. Virtually all species of freshwater fish will remain healthy at such feeding frequencies and there’s no danger of starvation.

If you give your pet fish more food than they need per mealtime, the leftovers sink to the bottom to rot, soon turning into nitrate.

Therefore, cutting back on the unnecessary food offerings will reduce both the rate at which fish produce waste and also the uneaten leftovers in the tank.

Leftovers are essentially wasted and can only serve as pollution to the aquarium’s water.

6. Optimize the livestock population for the size of the tank.

It helps to find the optimal balance between the tank’s size and the fish population.

Since more fish means more waste, you have to monitor their population from time to time so that the system does not become overwhelmed with nitrate.

Learn how to deal with the overbreeders and don’t get tempted to add more fish than the new system can handle before becoming polluted.

7. Vacuum 30% of the substrate every 3 days until it’s fully clean.

An effective way to fix high nitrate in your aquarium is by vacuuming the substrate because that physically removes food leftovers before they’ve had the chance to degrade.

Talking of substrate cleaning, it is advisable that you do it bit by bit in order to avoid destroying the beneficial bacteria that inhabit it.

Beneficial bacteria live on surface areas and the substrate along with your filter media contains the majority of the colony.

Vacuum 30 to 35% of the substrate every 3 days until it is wholly clean. This will give time to the beneficial nitrifiers to re-establish themselves.

Monitor your water’s reading during the process and add bottled bacteria such as Tetra SafeStart+ if you notice a suspicious spike in ammonia or nitrite.

You can research other such products if you’d like but SafeStart Plus is a good choice, in my opinion.

Anyway, though an interval of 3 days between the cleanings should be enough for a cycled tank with a running filter you can never be too careful about it.

In the end, you will have preserved the beneficial bacteria while the high levels of nitrate will be significantly reduced.

Note that this will only work if you’ve neglected the vacuuming for a long time.

If you’ve been diligent with removing food leftovers then this method may not show results.

8. Use a commercial nitrate remover.

There are critical moments when you can’t afford to spend hours changing small portions of aquarium water.

The commercial nitrate removers or denitrators are designed for these times.

You can buy one at a pet store locally or online.

There are several types to choose from, and each comes with specific directions to follow to achieve desirable results because they work in different ways.

A nitrate remover usually consists of some type of ion-removing media that you’ll need to put in the filter’s cartridge.

Commercial nitrate removers work at short notice and offer one of the best and quickest ways one can apply for nitrate removal from an aquarium.

Though they work quickly, all of them are designed to filter the water from the ions gradually.

This way these products avoid causing stress to freshwater fish and invertebrates.

Note that the way these products work in order to lower the aquarium nitrate levels is by physical removal of the contaminants.

Though it’s way easier than doing multiple partial water changes you will eventually have to “recharge” the media to keep it effective.

This method is for people who are willing to occasionally reload on inexpensive supplies.

The pro of using these products is that they’re really good for gradually reducing extremely high levels of nitrate that a 40% water change won’t be able to.

Using commercial nitrate removers is also great for when you don’t have a source of RO/DI water but your tap contains too much NO3-.

If your freshwater tank is in a pollution crisis then it may be a good idea to get a nitrate reducer.

My quick recommendation for a good product here would be API’s Nitra-zorb, but you can do some digging on your own if you’d like.

What PPM of Nitrate concentration is considered acceptable and safe?

The concentration of nitrate is calculated in Parts Per Million or PPM in short.

In the wild, the nitrate levels are generally hovering above 2 ppm.

In a closed system such as an aquarium, however, things can be different.

Some fish will adapt to higher nitrate content in their water, at least to a degree.

However, nitrate is a slow killer and the effects of its build-up will become apparent over time unless the spike was too sudden.

An aquarium could seemingly run with elevated levels of nitrate for months before its aquatic inhabitants start showing any symptoms.

Having said that, here are the safe nitrate levels for freshwater fish:

Levels of between 5 and 10 Parts Per Million (PPM) of Nitrate are likely to be safe for freshwater fish. Though many hobbyists consider levels of between 20 and 40 ppm to be acceptable, such nitrate contents are actually high and will inevitably cause health problems for the fish over time.

Sometimes more sensitive fish species will show signs of nitrate poisoning at just 20 ppm of Nitrate if the exposure was long enough.

Any level above 40 ppm of nitrate is way too high and poses a health risk to pet fish.

Toxic effects of prolonged exposure to Nitrate in fish

Prolonged exposure means that your fish have tolerated high nitrate levels for an extended period of time.

Stunted growth is one sign the nitrate has reached levels that are toxic to your fish.

The continued stress that comes with excess nitrate also weakens the fish’s immune system response, making its body susceptible to opportunistic diseases.

One of the conditions that often affect a poisoned fish is the swim bladder infection.

It’s a condition where the bladder responsible for the creature’s buoyancy gets filled with liquid instead of gas, causing the fish to swim sideways or upside down.

At one point life becomes a major struggle and the fish may perish if the water is not treated on time.

Other complications that come with Nitrate poisoning in fish include dysfunctional reproductive organs and damage to their nervous system.

The takeaway here is that high nitrate may not kill instantly, but it definitely can in the long run.

How fast this happens depends on the type of fish and how intense the exposure is.

But how would you know that your pet is battling with excessive nitrate?

Here are the visible signs of nitrate poisoning in fish:

  • A fish that is struggling to survive in unbearable nitrate concentration swims rather awkwardly, without orientation or equilibrium.
  • It eats less and less as it continues to lose appetite.
  • The vibrancy on its natural color fades as days pass and soon the fish turns dull and pale.
  • Prefers to lie on the tank’s bottom instead of swimming. If it attempts to swim, it acts weird and aimless.
  • Overall lethargic behavior.
  • A bent spine and curled body, often in a U-shape.

Why does this happen more often in Betta and Goldfish tanks?

While fish can live in more than 20 PPM of the same for a certain period, it is not ideal for many of them.

The reason why these consequences are especially common in Betta and Goldfish aquariums has to do with the stereotypical belief that because these are hardy species that can tolerate the harshest living conditions.

Betta fish and Goldfish are indeed tolerant of tough environments including higher nitrate levels, but only to an extent and not for a prolonged period of time.

To complicate matters, pet stores usually encourage beginners to keep these particular species of fish in small aquariums.

The fish soon have to contend with unhealthy conditions since the water in such small tanks gets contaminated way faster than in larger ones.

In fact, it’s way harder to maintain healthy water quality if you chose to keep your fish in a small 5-gallon tank, for example.

Eventually, these supposedly hardy fish suffer the same health problems related to prolonged exposure to high nitrate concentration.

Therefore, the simple reason why Goldfish and Bettas are usually the common casualties of nitrate poisoning is the false belief that they can live in any really small tank.

Furthermore, most people are not aware of how often they should feed their Betta and end up offering too much food on a daily basis. This can create even more mess in the aquarium’s water.

Over-exposure to higher nitrate levels is one of the most common reasons for a betta fish that lethargically lies on the bottom of its tank.

For a healthy Betta or goldfish keep the nitrate levels in their aquarium at 10 PPM or less if you want to see them happy and thriving.

Any level of above 20 ppm could turn out to be too high in the long run.

Future prevention of Nitrate build-up

So, what should you do differently to deter excessive nitrate levels in the future?

Master and practice the following:

  • Do not overfeed your fish.
    Feed your aquatic pets sparingly and give them just enough food to keep them going during the day.

    Feeding once every other day will keep your pet fish healthy and active, without polluting their water.

  • Do not overstock the tank.
    Keeping many fish varieties in large numbers in your tank may be lively, but you have to strike the right balance with the tank size.

    Overstocking the system is a sure way to raise the level of nitrate and will give you a hard time in the future.

  • Maintain a regular water changing schedule.
    The best control measure in case the nitrate levels keep rising in spite of your efforts is to change the water regularly.

    You should dilute the existing water over a couple of days instead of replacing the whole of it at once.

    A sudden change of the nitrate content in water, whether high or low, usually leads to a nitrate shock in freshwater fish.

  • Have lots of live plants.

    Having fast-growing live plants will help with keeping the nitrate concentration in check.

  • Physically remove organic waste.

    Find the time to clean the aquarium, remove the bodies of dead fish from the tank, vacuum the food leftovers from the substrate, etc. to minimize the build-up of organics in the water.

  • Have an emergency nitrate remover.

    It pays to have a bottle of denitrators around to save the situation should things get out of hand one day.

    Another option is to have a special filter with nitrate-reducing media.

  • Add a sump to act as a nitrate filter.

    Adding a refugium with some porous rocks and a grow light for algae can be one of the best long-term methods for keeping nitrate at bay.

  • Keep messy animals in larger volumes of water.

    There are some species of fish that are notoriously messy.

    These include Goldfish, Oscars, Eel-like fish, big plecos, and more.

    These animals produce more waste per body mass than most other aquatic pets.

    Keeping them in larger tanks will make it easier for you to dilute the nitrate pollution in time.

Last words

Lowering the nitrates in the aquarium is often overlooked and people often take action when there already are signs of poisoning.

This may not yield the best results, however, doing your research and acting quickly is key.

Remember that failure to fix the high nitrate levels in time could be deadly to your aquatic pets, and although nitrate is not as toxic as nitrite, it can still kill, even if slowly.

Leave me a comment below if you want to ask a question or to tell me about your experience.

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6 thoughts on “What Causes High Nitrate in a Freshwater Aquarium?”

  1. I have a 40 gallon tank with 4 black moores. It is about a month old. I did a 50% water change yesterday due to high nitrate. Still high. Feeding once a day. Checked water from tap (no nitrates) They seem to like eating the bottom of the floating plants. They are super cute, I’m a little worried about if I should do another 50% water change or stop feeding? Maybe feed only once every other day?

  2. Hi I’ve got a lemon goldfish about 15 years old . I think I’ve done everything wrong out of panic . Basically the water went green and the fish looked unhappy there was a big plant in the tank I took it out it was stacked full of old food I guessed the water was contaminated so I threw half out and put in fresh. The fish got what looked like fun rot so I got some stuff for that abd put it in then started reading up and realised I needed to do more so did a few water changes took out the gravel cleaned it added tap water treatment and something to get rid of nitrates etc … the nitrate is mega high still and the fish is mega stressed swimming into the dudes trying to get out … I’ve basically made it worse and have no idea what to do this fish is so stressed and hurting itself ….

  3. Not sure if you are still monitoring this article. I have a three month old planted tank. Ammonia 0, Nitrates 0, Nitrates 80-160. It has no fish. Occasionally, I will see a wilted leaf and remove it, but most of the plants are growing. My floaters have multiplied so much that they would cover the entire surface it I didn’t corral them. The lights are on 15 hours a day. There is not a spec of algae in the tank. The substrate is gravel. There is no organic material in the tank except the plants. I do not fertilize the tank, except I broke one root tab in half and buried in under two rooted plants. I can’t figure out where all the nitrates are coming from. Advice?

    • Hello Stephen,

      I monitor every article, it’s just that sometimes I’m too busy to respond in time and then forget.

      So… Your aquarium seems pretty enigmatic!

      It’s amazing that you have the lights on for 15 hours and don’t see algae, but that could be explained by the coverage of floaters, I suppose.

      Anyway, what brand of test kit are you using? Is it a liquid test kit or strips? If I take everything you’re saying at face value then, surely, it must be a false positive…

      One other possible culprit could be the water source but I don’t know what type of water could be so saturated with Nitrate.

      – Momchil

  4. This is very helpful. A wealth of info and I have learned a great deal reading this. Thank you so much!

    • No, thank YOU, Laura, for being my reader.

      Nitrate is one of those things that get overlooked in the aquarium hobby. I’m happy that there are responsible people who research even that.


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