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Cotton Wool Disease in Aquarium Fish: Signs & Treatment 

Cotton Wool Disease in Aquarium Fish: Signs & Treatment 

What is cotton wool disease?  | What are the symptoms?  | What are the causes?  | How can I help prevent it?  | How can I treat it?

Updated on February 03, 2023
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Reviewed by Don Spaeth
Petco’s National Aquatic Care, Education and Programs Manager
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Have you noticed a strange pattern on your fish’s body that wasn’t there originally? This is often a tell-tale sign of infection, one of the most common types of health concerns in aquariums. But infections can have many causes, including viruses, parasites, bacteria and fungi, and some look alike.

Cotton wool disease—a bacterial infection that causes white, cotton-like growths that can be mistaken for fungus—is a prime example. How can you tell if your fish has this illness, and what can you do about it? 

What is cotton wool disease in fish?

Cotton wool disease—also called saddleback and cotton mouth disease—is a bacterial infection that can affect freshwater fish. It’s caused by the bacteria Flavobacterium columnare, often referred to as columnaris. These bacteria naturally occur in freshwater aquariums but only infect fish under certain circumstances. If fish are unhealthy, stressed or have compromised immune systems, they can be at a higher risk.

It’s easy to mistake this ailment for a fungal infection because of its appearance, but it is not a fungus. This is a critical distinction, as bacterial and fungal infections are typically treated with different medications.

What are the symptoms of cotton wool disease?

The first symptom of cotton wool disease in fish is flat, pale patches or lesions on the body. Over time, these turn white or grayish in color and become furry, fluffy or cotton-like. The patches usually occur around the mouth, fins, gills and dorsal area on the top of your fish, although infection of the gills is difficult to detect as they are hidden from view. As the disease progresses, your fish may have difficulty breathing or may not want to eat or move.

Because this disease looks like a fish fungus as it progresses, you may need to consult your veterinarian for a diagnosis. They can look at your pet’s cells under a microscope and tell you what’s happening with your fish.

What causes cotton wool disease?

Cotton wool disease is caused by bacteria, but its presence doesn’t guarantee your pet will become infected. These bacteria can only infect fish with immune systems compromised by illness, an open wound or stress. Therefore, cotton wool disease is considered a secondary infection and not typically a threat to humans caring for fish with the disease. 

To find the true cause of cotton wool disease in your fish, you’ll need to determine the root cause of their stress or illness. Fish can feel stressed if they are bullied or harassed by other aquarium companions. It’s important to ensure the types of fish in your community aquarium get along. Check out our Freshwater Community Fish Care Sheet for more information. 

Poor water quality can also cause cotton wool disease in fish. Your aquarium water is your fish’s “air,” and unclean or incorrect water parameters can cause stress and decrease their ability to fight infection. Poor water quality can also create the right environment for columnaris bacteria to grow.

How can I help prevent cotton wool disease?

Because this infection typically only occurs in stressed or unhealthy fish, the simple answer is to keep your fish well fed and stress-free and ensure your water is clean and follows proper parameters. The bacteria that cause cotton wool disease thrive in warmer waters above 80 degrees, so maintaining the proper temperature is essential—most freshwater fish like temperatures between 72 and 82 degrees.

You also need to ensure the bioload in your aquarium doesn’t get too high. Bioload is the amount of aquatic life and waste produced; when it gets too high, nitrite, nitrate and ammonia levels will rise. Be sure to change out 10 to 20 percent of your water every two to four weeks and only use dechlorinated water in your aquarium. Test the water to ensure nutrient levels are appropriate after you perform water changes. Learn about creating a water care routine in our New Freshwater Aquarium Guide. 

It’s also important to quarantine any new fish before adding them to your aquarium. If they harbor the malicious form of columnaris bacteria, it can easily spread between fish. Set up a quarantine habitat where you can keep new fish separate for about two weeks. Use a filter and test, treat and maintain the water just as you would in your main aquarium.

Also, ensure you don’t put too much aquatic life into a single aquarium—this can cause them to over-compete for resources or space. The amount of aquatic life you should keep together depends on the size of your inhabitants, how much waste they produce, the size of your aquarium and your filter’s capabilities.

Finally, always remove any infected fish as soon as you notice signs of illness. Keep infected fish in a separate quarantine habitat so you can monitor and treat them while reducing the risk of cotton wool disease spreading.

How can I treat cotton wool disease?

This bacterial infection is typically treated with aquatic life medication but can be difficult to cure completely. You’ll want to start administering medication as early as possible. Because medications take time to take effect, fish with more advanced symptoms may not respond to cotton wool disease treatment in time to help them.

Cotton wool disease treatment also requires a hospital aquarium. This is similar to a quarantine habitat; except you’ll add treatments and medications. Another important distinction is that your hospital setup shouldn’t use chemical filtration, like activated carbon, which can remove aquatic medicine. However, if you remove the chemical filtration, you can use your quarantine setup as a fish hospital. A separate area is essential to prevent the spread of disease and ensure the treatments don’t harm the water quality of your main aquarium.

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