What Causes Brown Spot on Aquarium Plants?

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Aquarium plants require the same level of care that fish do, especially when it comes to water conditions and the nutrients available.

Caring for the plants is ultimately caring for the fish since aquatic plants are an important source of oxygen, food, and comfort for the fish.

The problem is that, when lacking the proper environmental conditions, plants can experience health issues.

These will come with various signs, depending on the underlying problem, but there’s one that’s present in almost all cases. We’re talking about brown spots present on the leaves.

These will often differ in size and color intensity but will always be an indicator that something’s not right with the plant. Identifying the cause is crucial to prevent the plant from dying.

In many cases, early measures can even reverse the process, allowing plants to make a full recovery.

Causes of Brown Spots on Aquarium

There are a few triggers for brown spots on tank plants, and all of these have the potential to kill the plant.

These include:

Poor Water Conditions

Dirty waters, in general, don’t really affect plants in an open system like a lake or a larger river basin.

That’s because the system is open, allowing water to move freely and dissipate the harmful chemicals associated with fish waste and dead matter accumulating in the water.

The situation is entirely different in a closed system like an aquarium.

Fish waste, food leftovers, and dead plant and animal matter will accumulate in the water and decay fast.

This dead organic matter will serve as food for bacteria, which will produce ammonia and nitrites as byproducts.

These are deadly chemicals capable of killing all forms of aquatic life, plants, and animals alike.

If your plant displays brown spots on the surface of the leaves, you may be dealing with ammonia burns.

The leaves may also display bent and contorted edges and will eventually fall off.

The issue here is the complete reliance on the filtration system. Many people will skip maintenance days or think that the filter alone can keep the system stable, which is false.

To keep the tank water clean, fresh, and safe for both fish and plants, you should:

  • Set up a robust filtration system – The type of the filter to use depends on how many fish you have, the species they belong to, how large the tank is, etc. You may need mechanical, chemical, and biological filtration to cleanse the water of floating particles, dilute dangerous chemicals, and support the tank’s biofilm. Make sure that the filter isn’t overly powerful not to damage the plants or disturb the fish.
  • Remove dead matter – You should manually remove fish waste when excessive, food residues, and dead plant matter or dead fish. Doing so will take some weight off of your filtration system and keep the environment cleaner and healthier.
  • Perform tank maintenance – Cleaning the tank walls, removing waste, and cleaning algae deposits are essential for a stable aquatic environment.
  • Regular water changesWater changes are necessary to prevent ammonia buildup, reoxygenate the environment, and keep the water clean for longer. The frequency of the water changes depends on several factors, primarily the tank’s size and the fish species you’re housing. Cichlids, for instance, demand more frequent water changes due to being extremely messy fish. The same goes for goldfish. You also need to change the tank water more often in smaller tanks than in larger ones. So, always adapt to your unique situation.

So long as the water is in pristine conditions, your plants will remain healthy and thrive, provided nothing else disrupts that balance.

Nutrient Deficiency

Plants extract their nutrients from the soil (tank substrate), and the water and they require different nutrients based on their physiological necessities.

Some of the essential nutrients that the plants need to survive include:

  • Iron – Iron is essential, as it helps plants grow strong and larger. If the plant cannot find iron in the environment, it will eventually die off. Iron deficiency comes with early signs like yellow and discolored leaves slowly turning white with green veins. In extreme cases, the leaves will display brown spots, turn black, and die.
  • Manganese – This mineral is a key ingredient in the photosynthesis process and will support the plant’s growth along the way. Manganese deficiency looks similar to iron deficiency, with leaves turning yellow and white. The plant may also display holes in the leaves in advanced cases as it begins to die and wither.
  • Magnesium – Magnesium is also a major component in keeping the plant healthy and will influence its growth consistently. Magnesium works in tandem with iron since it transports iron throughout the plant’s system. Without it, the plant will also experience an iron deficiency shortly. It’s the same as with vitamin D and calcium since calcium requires vitamin D to ease absorption.
  • Potassium – Plants use a lot of potassium in general, so they need to have a consistent source in their environment. The problem is that the level of potassium in the tank will be influenced by a variety of factors, like pH, water hardness, and CO2 levels. The plant will exhibit tiny holes in the leaves, alongside discoloration and brown spots.
  • Nitrogen – Nitrogen is a byproduct of fish waste that the plants will consume daily to fuel their internal processes. The problem comes with not having enough fish in a heavily planted aquarium. The lack of nitrogen will cause the plants to turn yellow and display warped and dying leaves. Eventually, the plant will begin to decay.

There are also trace elements like boron or molybdenum that will play their role in maintaining the plant’s physiology.

But how do nutrient deficiencies occur in the first place? We will ignore the normal fluctuations which will occur in any aquatic setup.

We will also ignore the gradual ones deriving from lack of maintenance since these can be detected and addressed early.

Instead, we will discuss the sudden ones that are usually linked to improper water changes. More specifically, we’re talking about the water used during the process.

Most aquarists, including novices, now know not to use tap water since it contains chlorine, and this is deadly to fish and plants.

So, they will use RO/DI water instead, not realizing the new dangers coming along with these types. This type of water no longer contains harmful chemicals due to the sterilization process it has gone through.

The problem is that the same process is responsible for stripping the water of all its macro and micronutrients.

Using it to replenish 15-20% of your water tank will effectively dilute the tank water nutrients and starve the plants.

This is why you should always re-mineralize the water before using it.

Inadequate Light Conditions

Plants aren’t too picky about their lighting, but there is such a thing as too much or too little.

In essence, all plants require UV lighting to promote healthy photosynthesis, which, in turn, will boost their ability to absorb nutrients from their environment.

If there’s not enough lighting, the plant will no longer be able to feed or produce oxygen, for that matter.

In fact, it will consume oxygen in low-lighting conditions, which will affect the environment as a whole, fish included.

Too much light is also bad, whether we’re talking about intensity or overall duration during a 24-hour period.

The goal is to provide your tank plants with an adequate and balanced day/night cycle with moderate lighting during the day.

How much light your plants need depends on the type of plant and the overall tank setup.

As a general rule, you need to make sure that both the plants and the fish prefer similar lighting conditions. Otherwise, their needs might come into conflict, and one side will necessarily suffer.

Brown Algae

Algae will always grow in any aquatic environment, but there are ways to mitigate their expansion.

Algae aren’t necessarily bad for the environment, as they serve as food for some fish, and they do have their role in the ecosystem.

But they will become a pest when over-reproducing, spreading throughout the entire tank and suffocating the vegetation.

Brown algae are notorious for doing so. However, brown algae are not what they seem. These are actually not algae at all, but rather bacterial colonies spreading pretty much on every surface, including the plants’ leaves.

The microorganisms forming the algae-like formation are called diatoms, and these are basically bacteria.

Their presence will ruin the tank’s esthetics immediately, imbuing the water and the environment with a rusty and dirty look.

And that’s not the only problem. Brown algae will also cover the plants, limiting their access to nutrients and sunlight.

As a result, the plants will begin to starve and die off, unable to support its physiological processes anymore.

Brown algae are pretty easy to detect in the tank since they will not only cover the plants but also float freely into the water.

Dealing with brown algae is essential to keep the environment healthy and stable. Preventing the brown algae in the first place is even better.

We will discuss this aspect shortly.

Lack of CO2

CO2 is just as essential as oxygen to plants. Plants use CO2 during the daytime to fuel their internal processes and aid in photosynthesis. They will release oxygen as a byproduct.

Research shows that the more CO2 there is in the environment, the more effective the photosynthesis process will become, with the plant producing increasingly more oxygen.

The same effect takes place underwater, which makes things more difficult since CO2 is a gas, and supplementing an aquatic setting with a gas can be tricky.

Fortunately, there are some ways to do it effectively, as you will soon see.

Inadequate Substrate

The problem here is that all rooted plants will extract most of their nutrients from the substrate.

This is an issue since most tank substrates are not fit for nourishing plants properly. Even sand is inadequate since it isn’t particularly nutritious, to begin with.

Gravel is even worse since the particles aren’t small enough to retain any valuable nutrients. So, what’s the alternative?

Soil is a good option, but it isn’t always optimal, especially if you have substrate-digging fish like many cichlids and catfish.

The solution would be to use a plant-oriented substrate that’s specifically designed to nourish rooted plants.

You typically don’t need to invest in such a substrate in a fish-only tank. Planted aquariums, however, demand a different approach.

Make sure you’re getting the right substrate with the proper nutrient content that your plants need.

Can You Cure Brown Spots on Aquarium Plants?

Yes, you can cure brown spots on aquarium plants, but this largely depends on what caused them and how advanced the problem is.

Here are some effective measures to consider, depending on the triggers:

Manage the CO2 Levels

The solution is obvious. If the CO2 levels are too low, boost them up.

You can achieve this via several methods, such as:

  • Carbon injection – This is the most popular method of boosting the CO2 levels since it’s effective, easy to apply, and takes little time to complete. The injector will imbue the water with a carbon-based fluid that also acts as a fertilizer for the plants. You should see your CO2 levels come back to normal almost immediately. Depending on how fast the CO2 is drained from the tank, you may need to perform this procedure daily. If that’s the case, consider the following fixes.
  • A proper day/night cycle – Plants consume CO2 during the day to produce oxygen and reverse the process during nighttime. To keep the system going as intended, always allow your plants a period of darkness to keep the CO2 levels stable. Not enough lighting is bad for the plants, but so is too much.
  • Minimize the bubbling effect – You might want to eliminate air stones, and air pumps, lower the power of the filtration system and remove any over-the-top bubbling devices. These may look good, but they will actually speed up the loss of CO2 at the water’s surface.
  • Slow-growing plants – Some plants have an accelerated growth rate, causing them to consume a lot of CO2 in the process. Focus on Anubias, java moss, Phoenix moss, or Cryptocoryne (among others) since these are slow-growing plants with a more extended developmental phase. You can also diminish the light source to slow their growth even further.

These tactics should minimize the loss and consumption of CO2, keeping your plants safe and in good condition.

Manage the Brown Algae

There are some specific circumstances that will cause your brown algae to flourish.

Understanding what those are will inform you on how to manage them effectively.

These are, in no particular order:

  • Poor Lighting – To set things straight, there isn’t definitive evidence that poor lighting contributes to the development of brown algae. But there is some anecdotal evidence in the form of many aquarists experiencing some apparent correlation between the 2. So, make sure your plants get proper lighting during the day to minimize the risk of algae formation.
  • Manage phosphates and nitrates – Brown algae use phosphates and nitrates as food sources. The most common sources of phosphate and nitrate including decaying organic matter, food residues, fish waste, excessive plant fertilizers, pH buffers, etc. You can also include dead fish in the same category. This problem is easily fixed by sticking to a healthy maintenance routine and cleaning the environment regularly.
  • Manage silicates – Silicates are the main source of food for brown algae, so you can use this information to starve the bacteria. Live sand and live rocks are common sources of silicates, so avoid those if you’re experiencing brown algae problems.
  • Clean the algae manually – This is easier than you would suspect. You can use a piece of cloth and a sponge to clean the brown algae from any surface, including the plant’s leaves. Doing so will force the algae to disperse into the water, allowing the filtration system to pick it up.

Remove the Plant(s)

If nothing works and your plant seems to degrade even further with time, you might want to remove it from the environment completely.

It’s not worth keeping a dying plant in the water since it will no longer contribute to the system’s stability.

Furthermore, dead plants will promote the formation of algae and ammonia, which will degrade the environment even further.

It will also affect the fish since ammonia is poison to them.

How to Prevent Aquarium Plants Turning Brown?

Prevention is always key when discussing plant health and creating a thriving aquatic setting.

There are several strategies to consider in this sense:

Proper Filtration and Tank Maintenance

Keeping your tank water clean and well-oxygenated will keep the plants healthy and boost their growth and coloring.

The goal here is to remove floating particles and debris, clean fish waste and food residues, and ensure stable water parameters

Doing so will help your plants ‘breathe’ better and synthesize more nutrients from their environment.

Adopt a thorough and stable maintenance routine where you remove waste and change 15-20% of the water weekly.

This approach will also benefit the fish since it will keep their habitat clean, rejuvenated, and fresh over the years.

Avoid Overstocking

Overstocking in fish is bad enough due to instigating violence and leading to fish stress. You don’t need to overstock plants as well to make things even worse.

Plants will compete over the same resources in the tank. If there are too many of them in a tight space, the CO2 levels will be insufficient for all plants.

The same goes for any other nutrient. Sure, heavily planted aquariums look great, but they’re not really safe for either the plants or the fish.

Monitor Nutrients

Water nutrients will fluctuate for a variety of reasons, especially during water changes. I suggest monitoring water nutrients to ensure a stable and healthy environment for your plants.

At least keep an eye on the macro-nutrients like iron, potassium, and magnesium, if nothing else, since these are essential for plant health.

Also, use a nutrient-enriched substrate for rooted plants.


Most aquarium plants are hardy and resilient and won’t mind the occasional environmental changes.

However, as we have already discussed, there are some problems worth considering in the long run.

I would say that the 2 most prevalent issues are low CO2 levels and nutrient deficiency.

Keep these parameters in check, and your plants will thrive in the long run.

Author Image Fabian
I’m Fabian, aquarium fish breeder and founder of this website. I’ve been keeping fish, since I was a kid. On this blog, I share a lot of information about the aquarium hobby and various fish species that I like. Please leave a comment if you have any question.
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