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Why Are My Aquarium Plants Turning Brown? Causes And Cure

Planted aquariums are a huge favorite of mine, but I’m the first to admit that maintaining aquatic plants is a lot harder than raising tropical fish. I’m often asked, “why are my plants dying or turning yellow?” If you’ve ever wondered why your aquarium plants are turning brown or not thriving, then this guide is for you!

Troubleshooting Problems With Freshwater Plants

A green beautiful planted tropical freshwater aquarium with fishes

The most common reason for yellow, brown, or black leaves on aquatic plants is poor water quality. Plants are far more sensitive to their water conditions than most animals and show signs of stress when things are out of balance. In community tanks, plants act as the canary in the coal mine and send out early warning signs.

Plants rely on the nutrients in your substrate and floating in your water, and depend on your aquarium lights to give them the ideal spectrums of colors for photosynthesis. When your plants are not thriving, that’s a sign there’s a bigger problem with your tank. How do your troubleshoot, identify and fix the issue to bring your plants back?

How to Tell if Your Plant Nutrients Are Out of Balance

One of the first places to start looking for the problem is by examining your overall water quality. In addition to checking your pH, water hardness and ammonia levels, you should also examine your plants and see if you can spot symptoms that point to an excess or lack of specific nutrients or trace elements.

Macronutrients

Macronutrients are those most critical to healthy plants and that aquarium plants need in large amounts. You’ll often find these nutrients in balanced plant fertilizers, but that doesn’t mean you should just add fertilizer anytime you have a problem.  Here are the most important macronutrients and how they impact your plants.

Carbon

If you’ve ever taken an organic chemistry class then you already know that without carbon (C), there’s no life on planet Earth. Every living creature depends on the abundance of carbon for survival. Plants mostly utilize carbon from carbon dioxide (CO2), since it’s an essential component of photosynthesis.

Signs of Carbon Deficiency

Carbon deficiency is a very common problem in planted aquariums. In fact, this is the most likely reason I’ve run across for poor plant growth and a failure to thrive. Some of the signs that your tank needs more carbon to include:

  • Stunted or weak plant growth
  • Pale or yellow leaves
  • Yellow plants with dead leaves leading to dead plants
Adjusting CO2 Levels in an Aquarium

Since CO2 is a gas, it can be a little harder to supplement in an aquarium than the other macronutrients. Altering your CO2 levels can also change your water’s pH, so keep an eye on that as you’re making adjustments. Some techniques to increase the available CO2 in your tank include:

Primus 160 CO2 System w/ Disposable CO2 Tank for Planted Aquaria up to 40 Gallons - Dennerle

  • Use a carbon injection system or add a carbon-based liquid fertilizer to the water every day
  • Cycle the lights on and off during the day to allow the CO2 from your fish and bacteria to naturally increase the levels in the water
  • Choose slow-growing plants and reduce the amount of light that your tank gets to slow down your plant’s photosynthesis, allowing CO2 to build-up naturally
  • Reduce your water currents and remove bubbling devices to slow the loss of gaseous CO2 from your tank’s water

Phosphorus

Phosphorus (P) is also a tricky macronutrient to manage, because plants can suffer when there is a deficiency but also struggle if there’s too much. Water testing kits measure the inorganic phosphates in your water, but can’t detect the organic ones. The ideal levels for a planted tank are right around 0.5 ppm (mg/L).

Deficient Phosphate Levels

hands of aquarist planting water plant echinodorus in new aquarium

Phosphates (PO4) are usually present in tap water and added via the carbon filter media, fish foods, buffering solutions and aquarium salts. Organic phosphates are produced by decaying plant materials, food scraps and fish waste. When your phosphate levels are too low:

  • Mature leaves develop yellow patches that disintegrate, leading to large, ragged holes in the leaves before they fall off and die
  • If your plant’s new leaves are quickly turning yellow and dying, you probably need to check your phosphate levels and add a balanced fertilizer
Excess Phosphate Levels

Higher organic phosphate levels can increase plant growth up to a point, but also often lead to algae outbreaks, especially the dreaded green spot (GSA) and green water algae (GWA). This usually happens when you skip water changes and inconsistently maintain your tank. If there’s too much phosphate in your water:

  • Your plant’s leaves may turn brown or black, and the plants start dying
  • Test your phosphate and ammonia/nitrate levels, do a 50% water change and really vacuum your substrate to remove decaying materials!

Nitrogen

Nitrogen Cycle Diagram

Nitrogen (N) is the most abundant element in our atmosphere, and both plants and your good aquatic bacteria rely on the nitrogen in your tank to grow and thrive. Aquatic forms of nitrogen include nitrate (NO3), ammonia (NH3) and ammonium (NH4). These are also essential components of the nitrogen cycle in a fish tank.

Deficient Nitrate Levels

One advantage of planted aquariums is they don’t usually have problems with excess ammonia or nitrate levels because the plants use these nutrients before they can cause harm to your fish. However, in densely planted tanks with few fish you may not have enough waste to keep the cycle moving. Low nitrogen can lead to:

  • Mature plant leaves that turn yellow and fall off
  • Yellow or stunted new growth
  • Warped or reddish-colored new leaves
Excess Nitrate or Ammonia Levels

This is a less-common problem in planted tanks, but if you add a lot of plants to a new tank before it’s properly cycled, you may not have enough of the good bacteria to break down the fish’s waste products into usable nitrates. Your new plants may turn yellow, brown or black and die. I talk more about how to handle new tanks below.

Potassium

A green beautiful planted tropical freshwater aquarium with fishes

Potassium (K) is a critical nutrient for plant growth and one of the more common to have deficiencies in, since plants use it in large amounts. It’s a little tricky to fix since your potassium levels fluctuate with and are influenced by your CO2, pH and water hardness levels. Most planted tanks benefit from potassium supplements:

  • When your potassium is too low, you’ll usually notice tiny yellow pinholes in your plant’s leaves
  • You may also see yellowish discoloration along the edges of the leaves, but unlike the magnesium-deficient plants below, the leaf will look normal other than the yellow edges

Magnesium

How To Reduce Nitrate In Your Aquarium - Aquarium aquascape with fishes.

Magnesium (Mg) is one of the most important nutrients and lends a hand in keeping your plants healthy and green. Low magnesium can also resemble iron deficiency, and the two go together, since a lack of magnesium reduces the amount of iron your plants can absorb. You’ll often have to fix the problem with a good fertilizer.

  • If your magnesium is deficient, established plants turn yellow along the edges or develop yellow spots on the older leaves
  • Magnesium deficiency can also look similar to a deficiency of potassium, but the veins of the leaves usually remain green even as the leaf turns yellow

Micronutrients

Plants also utilize other trace elements in smaller quantities, such as iron, manganese, boron, and molybdenum. Between your substrate, fertilizers and water changes you’ll usually have these nutrients in sufficient supply. The most common deficiencies in micronutrients are low iron (Fe) and manganese (Mn) levels.

Iron

Seachem Laboratories Flourite Premium Gravel - 7Kilograms / 15.4 lbs

Iron-rich substrates like Flourite and iron-containing fertilizers are a great way to prevent deficiencies and support lush plant growth. It depends on the form, however, as some types of iron are not soluble and are thus unavailable to your plants. In the early stages of iron deficiency, you’ll see symptoms like:

  • New growth and tips of leaves look pale, yellow or white
  • Mature leaves turn pale yellow advancing to transparent or white, with green veins showing through (chlorosis)
  • In advanced cases of iron deficiency, the leaves and plants will look very stunted and eventually turn black as the tissues turn necrotic and die

Manganese

background of the aquarium with green plants

Manganese is vital for your plant’s metabolism, and deficient plants often have problems with their photosynthesis and growth. Plants suffering from low manganese levels often have similar symptoms to those with iron deficiencies. Luckily, most iron-rich fertilizers contain traces of manganese as well. Symptoms include:

  • New growth looks pale or yellow
  • Leaves develop yellow spots, leading to ragged holes between the leaf’s veins

Additional Causes for Brown Aquatic Plants

Nutritional deficiencies are not the only reason for aquatic plants to turn brown or die. As I mentioned above, your overall water quality, lighting conditions and substrate also play a role in the health of your plants.

Poor Aquarium Maintenance

detail of man's hand coming out of the aquarium during his cleaning. Household chores concept

I learned the hard way that planted aquariums require more frequent water changes than fish-only tanks. When I started my first planted community I made the mistake of doing water changes only once a month, like I always had done. Not surprisingly, my plants didn’t fare well at first.

Once I started doing more frequent water changes and added ammonia-removing media to my filtration systems, my plants started shooting up. I didn’t know how to diagnose specific nutrient deficiencies, so I used a balanced fertilizer after each water change. This could be all you need to do to solve a brown plant problem!

Inadequate Lighting Conditions

Aquarium with fishes on dark background

Back in the old days, if you wanted a thriving planted aquarium you needed to invest in the best light set-ups and frequently replace the bulbs. With modern LED aquarium lights things have gotten cheaper and you won’t need to swap out the diodes as often. As long as your plants get the right spectrums of light, they should do well!

It depends on your plants, however. Easy-to-grow aquatic plants often don’t have very strict requirements. If you’re planning on a densely planted or aquascaped tank or to want more challenging plants, you may need a higher quality light fixture to support their growth. Excess light and nutrients can cause algae problems, though!

Inappropriate Substrate for Planted Tanks

Sand dunes isolated on white background

For setting-up fish-only communities, your substrate is usually not a critical choice to worry about.  But planted aquariums rely on the substrate for nutrition and to support the bacterial colonies that break ammonia down into usable nitrates. If you choose a sandy substrate, you may actually prevent your plants from thriving!

Sand and colored aquarium gravels lack trace minerals and nutrients to support lush plant growth. Sand also compacts down easily, leading to dead zones in your aquarium and substrate that are devoid of oxygen. I recommend using a substrate designed for planted tanks, and boost the effect with a balanced fertilizer!

Plant Symptom(s) Possible Cause(s) Remedy(s)
Leaves turning brown/black
  • Too much phosphorus/high phosphate levels
  • Too much ammonia/high nitrate levels
  • Advanced iron deficiency
  • Water changes and new maintenance schedule
  • Improve water conditions with better filtration/filter media
  • Use an iron-rich fertilizer
Mature leaves turning yellow
  • Light deficiency
  • Potassium or magnesium deficiency
  • Carbon deficiency
  • Deficient nitrate levels
  • Improve lighting
  • Use a balanced fertilizer
  • Increase CO2 levels
  • Add fish or use a balanced fertilizer
Spindly or weak growth
  • Carbon deficiency
  • Nutrient deficiency
  • Light deficiency
  • Increase CO2 levels
  • Use a balanced fertilizer
  • Improve lighting
Growth stops/plants dying
  • Low water temperatures
  • Carbon deficiency
  • Advanced iron deficiency
  • Use aquarium heater to stabilize the temperature
  • Increase CO2 levels
  • Use an iron-rich fertilizer
Large Holes in the leaves
  • Poor water quality
  • Excess nitrate levels
  • Improve water conditions
  • Water changes and new maintenance schedule
Brittle leaves, yellow new growth or yellow spots on leaves leading to holes
  • Magnesium deficiency
  • Iron or manganese deficiency
  • Potassium deficiency
  • Excess pH levels
  • Use a magnesium supplement
  • Use an iron-rich fertilizer with trace minerals
  • Use a balanced fertilizer
  • Check pH levels and correct
Leaves or whole plant turning white or transparent
  • Iron or manganese deficiency
  • Light deficiency
  • Use an iron-rich fertilizer with trace elements
  • Improve lighting

Other Common Problems with Planted Aquariums

When your aquarium plants are turning black or dying, the first things to consider are a deficiency of nutrients, water quality problems or a lack of sufficient light to support plant growth. But those are not the only reasons folks struggle with planted tanks!

New Tank Syndrome and Plant Problems

Close up shot of hands putting plants on the low water aquarium.

One really common error I made myself was adding plants to a new aquarium that hadn’t completely cycled. Since your plants rely on the populations of aquatic bacteria to break down ammonia into nitrate, a tank that is cycling often has spikes and crashes in their levels, and these rapid swings can stunt and kill delicate plants.

Until you have stable populations of good aquatic bacteria, which can take roughly 3 to 6 weeks, it’s best to skip dense plantings and instead pick a few fast-growing and hearty test-plants like hornwort. A few bunches can quickly use up nutrients to help prevent algae outbreaks, and they’re tough enough to make it through the spikes.

Brown Spots on Plant Leaves

Not all brown plant problems are tied to nutrient fluctuations, at least not directly. If your plants start developing rusty-colored brown spots on the leaves, especially if it’s a new tank that’s still cycling, you’re likely dealing with an outbreak of brown algae instead of a nutrient deficiency. If the spots rub off and feel a bit gritty, it’s algae.

background of the aquarium with green plants

If you’re wondering how to clean brownish spotted leaves, the truth is you might not need to bother. Brown algae usually appears in newly cycling tanks and goes away on its own once the nitrogen cycle is established. You can wait the problem out, do extra water changes to lower the nutrient levels or get an algae-eating Otocinclus!

Conclusion

It’s easier to prevent your aquarium plants from turning yellow, brown or black than it is to bring them back from near-death. If you’re diligent with maintaining your water quality, choose the proper substrate and lighting conditions for your type of plants and regularly apply a balanced fertilizer, your plants will likely stay green!

When and if plant problems do crop up in your tank:

  • Troubleshoot the problem by examining your plants and test your water for the likeliest suspects
  • Do a water change or two and be sure your filtration system and lights are in good condition
  • Use the right type of fertilizer (if needed) and change-up your maintenance schedule to get things back on track!

Aquarium Plants Turning Brown? A Short Guide to Planted Tank Problems - Infographic

Jen has more than 30 years experience as a biologist, aquarist, and fishkeeper. She is an expert in setting up new tanks and maintaining naturally-planted freshwater habitats, and has experience raising a wide variety of aquatic species.

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