Aquarium Fish Diseases: Fungus and Bacteria


Diseases, which most of the new fish keepers and the fish they are keeping sometimes suffering because of them. Even if you are an expert with lots of experience, you may also face a disease that you never saw before.

For fish diseases, it is very important to diagnose and determine the disease correctly such as in humans to start the proper treatment. To make this, a knowledge base is required. So, in this post, you can find some helpful information for reference. We tried to include as much as possible and correct info in this post but still, you may find more detailed data online in case you need to diagnose and treat any disease. We will also keep posting about diseases to create a large database for hobbyist’s reference here.


Cotton Wool Disease


Fungus spores are found in all fish tanks and other fish environments. That is why fungal infections are common among fish. Cotton wool is a fungal infection that spreads when the spores of fungus quickly colonize and create infections on the fish. White fluffy appearance is characteristic of fungal infections. When the fish is injured or stressed or is already sick with any other disease, catching a cotton wool infection chance increase. The cotton wool infection becomes grey or even red when it is left untreated.

The fish has a natural mucus layer on its body which protects it from fungi and bacteria. But when this layer is disrupted and the immunity system weakened the spores of fungi find the chance to colonize and infect the fish.


• Injuries caused by fights among the fish or because of accidents in the aquarium leave the fish vulnerable to fungal attacks.
Parasites in fish increase the chances of cotton wool fungal infection.
• Rough handling disrupts the mucus layer on the fish’s body and it is more prone to cotton wool fungus.
• Water quality or temperature changes increase the spread of fungus spores.
• Leftover food is the best cultivation bedding for the fungi especially if you have not added snails in the aquarium to eat the leftover food and other organic matter.
• Decomposing dead fish or other organic material in the aquarium increases the population of fungus.


• Wool-like patches of brown or grey color on the mouth, fins or body of the fish.
• Fish loses its active social behavior and spends most of the time hiding or holding still.
• Fish eats less or does not eat at all. These signs usually appear after the fungus is fully developed on the body.


• Common treatment is using a commercial fish fungus medicine or Malachite Green. As with all treatments should be applied the dosage matters. So, it is best to know dosing amounts before using any of these treatments.
• For treating with malachite green, add 0,10 mg per liter. Three days later make %50 water change and repeat the dosage. Treatment should be done at least three times with intervals of three days.
• Salt bath in a separate tank is good for the infected fish. Mix one tablespoon of salt with 4 liters of water to prepare the salt bath.
• Anti-fungal agents are also a good option for the treatment. Follow the instructions written on the label for correct doses.
• Follow the treatment plan as directed by the vet. Gaps in the treatment or insufficient treatment can make the fungi stronger and more resistant to the treatments.


• High-quality water is important for saving the fish from fungal attacks. Keep filtration at its best.
• Regular water changes to remove the possible bacterial or fungal growth in the fish environment.
• Keep the aquarium well-oxygenated.
• Observe for any skin cracks, scratches or wounds and treat them instantly before an infection appears.
• Remove uneaten food from the aquarium. It is better to feed the fish in the right proportion to avoid leftover food.
• Do not combine more than one method for the treatment of any health issue in your fish.
• Complete the treatment as it is directed by the vet or instructed on the medicine labels.

Fish Fungus


The fungus is made of fine threads called hyphae. These create white or grey patches on fish like cotton wool. Saprolegnia and achlya are the most common types of fish fungi that develop in an aquarium. The spores of Saprolegnia are highly resistant to chemicals or drying which helps them spread fast and in most aquariums. Freshwater fish is more prone to fish fungus than saltwater fish because of the suitability of the freshwater environment for fungal growth.


This fungus includes species of Saprolegnia and Achlya also called water mold. Organic material like leaf litter, feces, and leftover food causes this fungus to spread. Saprolegnia in start makes small, focal infections. But it spreads rapidly over the gills than the whole body of fish. As it spreads, healthy tissue is also destroyed and the fish weakens.


• Fungus sprouts in decaying dead fish, rotting organic matter, dead or unfertilized fish eggs. Millions of spores of fungus spread in the water and invade the organic material and living tissues. When the fish mucus layer is damaged, fungus infection in the fish spreads faster.
• Injuries on the fish body also encourage fungus development.
• Water chemistry changes also increase fungal infection risks.
• Body ulcers or itch in fish allow the spores of fungus to enter the fish and infect it.
• When the tank water becomes full of excessive fish waste, ammonia, nitrites and bacteria, the fungus develops and spreads in the fish.


• Fungus must be removed through good and fast treatment or it will spread more and the fish may die.
• Organic dyes like malachite green are good for fungus treatment. For most community fish, this treatment is safe. But do not use it if your aquarium has stingrays, mormyrids, shrimps, snails, or other invertebrates.
• Fungus is not seriously contagious. You can transfer the infected fish to another tank for separate treatment if the other fish are not infected in the tank.
• Tea tree oil is less toxic for treating fungus in fish. But it is more effective if used as a precautionary or preventative method for conditions when fish are vulnerable to fungal infection because of skin or fin damage or injuries.

Egg Fungus


The fungus can spread on fish eggs also. Mostly the unfertilized eggs only get infected by fungus. Some fish like cichlids eat their unfertilized eggs but you can also remove them with help of a pipette. They look opaque and different from healthy eggs in case of infection. If they are not removed, the fungus can develop in them and can transfer to the healthy fertilized eggs and destroy the whole batch.

Chemical Prevention

Lower the pH because the fungus does not grow in a low pH environment.

• Use aquarium chemicals to lower the pH of the tank or use liquids of Blackwater Extract. The leaf litters add organic acids to the water which inhibits the fungus growth as well.
• The most common chemical for lowering the pH level is methylene blue and Acriflavine. But keep methylene blue away from your hands and clothes because it leaves blue stains. Methylene blue and Acriflavine can also kill the fry if not properly dosed. The best thing to do is to use them as a dip or do a short bath treatment. Do not add them in a well-cycled balanced tank. Treating the egg fungus in a separate tank is the best practice. After completing the treatment add an activated carbon filter to remove the chemicals and remains of Acriflavine because they can kill the fry after the egg hatching.
• A few drops of sodium chloride solution in 20 gallons of water can be helpful to prevent egg fungus.
• Pimafix is a natural tincture and not a synthetic chemical. This is also a good choice for preventing fungus in a fish tank.

Safer Methods

• Keep the aquarium water clean.
• Provide good filtration.
• Change the water regularly.
• Remove the gravel from the tank because it traps the organic detritus and fungus establishes there. This is an option when mass breeding of fish is desired. For the hobby aquariums, it is not necessary if the filtration is properly working and the tank cycle is settled well.
• Do not mix species that might fight and injure one another to enable fungus development on the injured tissue and spread in the tank.
• Water quality must remain constant at the level necessary for the type of fish.
• Remove the organic matter, dead animals and leftover food instantly and use gravel cleaners during water changes. Give your fish enough food to consume all and not leave some.

Mouth Fungus


Contrary to its name, mouth fungus is a bacterial infection normally associated with the head and not only the mouth. Another common name for this is columnaris. It attacks gills, jaws, faces, etc. But, in some cases, it can develop on fins and the rest of the body also. The short tufts in grey or off-white color distinguish it from other fungal infections. Untreated long-term mouth fungus can produce lesions and sores on the head and flanks of the fish.


These bacteria are present in all aquaria and do no harm unless they find chances to feed on tissues and living cells; then, reproduce and spread fast. Their actual function is breaking down the organic material in the tank and converting it into inorganic material that the biological filter bacteria can further process in healthy aquariums.

Naturally, the immune system in the body of fish can fight the invading bacteria if they enter in a wound on its body but if the fish is suffering from a poor immune system due to poor diet, stress, and poor environmental conditions, the attacking bacteria find a foothold in the body of the fish.

Therefore, whenever mouth fungus appears, the aquarist should check the fish and be sure they are not fighting or nipping each other. And all the fish are being maintained in the appropriate social groups, with a properly balanced vitamin-rich diet and the water quality is satisfactory as per the fish requirements.

Fish suffer from mouth fungus when ammonia or nitrate amount increases in the water. This is because of depleted oxygen and changed chemistry of the water increasing the population of bacteria.


Mouth fungus develops slowly unlike fin rot. But some strands of mouth fungus are pretty fast and they can kill a fish within a few days after appearing. On-time diagnosis and instant treatment are necessary for saving the fish.

• Use antibiotics that are effective against gram-negative bacteria like kanamycin.
• Get antibacterial medicine phenoxyethanol and add 100 mg per liter in the water for 7 days.
• Use nifurpirinol/nitrofurazone 0.2 mg per liter for 5 days.
• Use tea-tree oil for treating the isolated fish for bacterial infections.

Note: Above mentioned treatments are proper for separate applications. In case one treatment is not effective make sure to make at least %50 water change and filter the water with active carbon at least 24 hours before using another treatment chemical.

• Maintain the fish and the tank properly throughout the time of treatment with regular cleaning of the tank and provisioning a healthy diet to the fish. Make large water change after treatment and use activated carbon filtration.
• Keep water chemistry and quality up to the standard level.
• Separate aggressive fish from the community if they habitually fight with other fish.
• Isolate the infected fish from the aquarium and treat it in a separate tank.
• Salt is not a useful treatment but rather a preventive method. Use 1 oz per US gallon but most freshwater fish are not tolerant to salt. If you have mollies or guppies, go for this method as they are tolerant to salt.


• Keep the fish tank well-maintained, clean and at the right temperature.
• Do regular water changes to wash out or reduce the population of any present bacteria.
• The set-up should be correct according to the normal standards of the fish requirements.
• Choose the fish species for the community that can live together without fighting with one another and also stays healthy in the water quality, temperature and chemistry that you have set up.
• Do not keep betta fish in a non-heated aquarium.
• Do not keep Goldfish in an overstocked or unfiltered aquarium because they get infected in such kind of aquarium.
• Cichlid fish is aggressive and fights with their jaws. They must be kept as single species or other with other proper fish.


Aeromonas Infection


Aeromonas is a bacterial infection in fish. This is one common bacterium among many that are called Aeromonas salmonicida bacteria. When the water cleanliness level drops and the nutrition become poor, the bacteria find the chance to take over and there may appear red ulcers all over the fish body. It attacks Koi and Goldfish mostly and other warm water and freshwater fish species. When this infection is severe, it may kill the fish.


Aeromonas salmonicida bacteria attack several systems in a fish body. The symptoms include:

• The fish’s eyes become larger than their normal size (exophthalmos)
• Fluids gather in the abdomen of the fish (ascites)
• The kidneys are damaged
• Fish fins are ragged
• The body becomes red and the internal organs, gills, fins and tail develop hemorrhagic spots. Some fish suffer from ulcers on their gills and skin.


The cause of the infection is the bacteria Aeromonas salmonicida but the following environmental changes put the fish vulnerable to the infection:

• Skin cracks; broken or ripped fins, injuries on the body due to fish fights or any other damage on the outer body.
• Sharp changes like sudden rise or fall in the temperature of the water.
• Rotting leftover food or any other organic matter in the fish tank.
• Insufficient nutrition or malnutrition.
• Improper water chemistry which does not suit the fish.


For sores and ulcers follow the following treatment tips:

• In mild condition, give the fish bath in a separate tank, water mixed with sodium chloride or/and Magnesium sulfate.
• If the sores are becoming bigger and deeper, swabbing or dripping Methylene Blue directly on the ulcers and sores is highly effective.
• In case the condition seems out of your control or understanding, consult a specialist and he will prescribe antibiotics.

Pseudomonas Infection


Pseudomonas bacteria are aquatic bacteria and are also called ulcerous bacteria. It’s common among fish species. They develop in fish ponds where gravel, plants, and food are together found. Transferring fish from such a pond transfers the bacteria to other tanks and aquariums. This infection can kill the fish when it is not treated.


Small dark spots cover the infected fish’s body. After some time these spots change into little round red ulcers. These ulcers look like the bites of Argulus – a fish louse. An autopsy of the dead fish can reveal intestine inflammation. These ulcers give chance to other bacteria, viruses, fungi a path to the internal organs. If the sick fish gets weaker, Achlya and Saprolegnia fungi may develop over the ulcers.


• Add bicillin-5 – 500,000 U per 100 L. Repeat dose 6 times bi-daily basis and make water changes (25%).
• Use of white Streptocide or Biomycin can be used over the ulcers.
• Chlortetracycline 1,5 g per 100 L. Dose 4 times after every 7 days. Make water change before repeating the dose.
• Prepare a separate tank for bathing the infected fish: potassium permanganate (KMnO4) – 0,5 g mixed in each 10 L of water. Keep the fish in it for 15 minutes; do not exceed total bathing twice.
• Add Basic Violet K – 0,002g in each 10 L of water. Keep the fish in it for 4 days. Give the fish bath for once in (OTIMM). Oxytetracycline hydrochloride (OTIMM) is specially made for aquatic animals and is available at local stores. The method of use is written on the pack.

There are also commercial medicines (either injectable or in solution forms) that can help better and faster to cure the infected fish, they are: (use these medicines upon the prescription of a certified vet only)

• Aquarium Pharmaceuticals Triple Sulfa
• Aquarium Pharmaceuticals E.M. Tablets
• Sera Baktopur direct
• Aquarium Pharmaceuticals Furan-2
• Streptocide
• Bicillin-5
• Aureomycin (chlortetracycline) hydrochloride
• Biomycin


• Take great care when transferring fish from a pond to a new aquarium.
• Take good care of the quality and chemistry of the water in a fish tank, aquarium or pond.
• Give your fish a nutritious and healthy diet.
• Keep the tank clean and change the water regularly.
• Keep the water parameters as per the requirements of the fish.

Flavobacteria Infection


Flavobacteria infection is also known as Bacterial Gill Disease in Fish. It is more common for small fish like salmonids but other aquarium fish also can suffer from it. The disease can claim the life of the fish because the infection can deteriorate the cells and kill them. This infection can attack fish at any age.


• Flavobacteria infection attacks the gill that is why the respiratory system of the fish is affected.
• Difficulty in breathing. Fish swims close to the surface trying to get enough oxygen.
• Loss of appetite.
• Some infected gills show signs like red gill tissues, swelling, and gill deformities.
• Patchy gills or patchy bacterial growth on the gills.


• Overcrowded aquariums become an easy breeding ground for Flavobacteria.
• Low water quality allows the bacteria to spread faster.
• Organic waste especially when it is in big amounts.
• Water temperature hikes.
• Increased ammonia level.
• The weak immune system of the fish. Strong and healthy fish does not get affected by the infection.


• First, the disease must be treated with a change in the environment.
• Improve the living condition of the fish.
• Increase the size of the tank and give them more space for living.
• The most important is cleaning the tank. Change the water and siphon the gravel. Clean the filters and improve filtration and aeration.
• Apply a treatment of salt water (1 tablespoon for 20 liters) and potassium permanganate to help the infected fish to recover.
• Treat fish with a salt bath (1 tablespoon for every 4 liters) for 30 minutes.
• Fish bath in Merbromin(highly effective), Methylene Blue or Potassium permanganate is very effective on columnaris.
• Antibiotic therapy is also applied to treat secondary infections as well.


• Maintain the best hygienic living conditions for the fish.
• Try to clean the water from all sorts of organic waste as much as possible.
• Never let the aquarium get overcrowded because the fish needs space to swim about freely and without stress.
• Keep the temperature consistent.
• Clean the filters every month or change the filter wool.
• Develop a good and nutritious feeding routine.

Flexibacter Columnare (Columnaris)


Flexibacter Columnare is a bacterium that causes a fish disease known as Flexibacter columnaris or Flex. This disease builds up white fungus on the affected part of the body of a fish. Flexibacter exists in all sorts of fish aquariums but does not appear as a disease until the water quality drops or the fish suffers from stress and accordingly the immune system gets weaker. This can be fatal to fish if not treated on time.


Uneaten food when left in the fish tank elevates the level of nitrate in the water and also provides bacteria to over breed. The oxygen decreases and the water temperature rises. This especially occurs fast when the tank water is not clean and the water changes are not regular or insufficient. The growth of Flexibacter increases in the water and starts attacking the fish.

Flexibacter is contagious and spreads fast among the fish even if they are healthy. A human contacting with an infected tank and uninfected tank can spread and carry the disease between tanks. The most favorable condition for the fast bacteria spread is a rise in the water temperature.


• White spots develop on the head, fin edges, and scales of the fish.
• Symptoms get worse if fish is left untreated. Columns of bacteria develop on the fish skin.
• Some parts of the fish body become discolored.
• Flesh rots starting from the fins and tail areas.
• Fish breathes rapidly.
• Fungus-looking growth around the mouth.
• Lesions appear on the fish body.
• The disease looks like fungus and it is important to have an expert check the fish for the right diagnosis.


• Treatment involves treating the fish and the tank both.
• Add Terramycin to the fish food and feed it to the infected fish.
• Treat the tank water with Potassium Permanganate, Tetracycline, Furan, Copper Sulphate, or Kanamycin.
• Change the water in the tank regularly and clean the fish tank thoroughly.
• Keep the water quality high.

Fin Rot


Pseudomonas fluorescens is a gram-negative rod-shaped bacterium that causes the disease known as Tail Rot, Fin Melt or Fin Rot. It attacks the fins and tail of the fish especially if they have any skin injury because of an accident or fight with other fish. The edges discolor and become lighter or darker. The fins and tail start deteriorating and if the infection is not treated on-time, the fins and tail fully rot and the infection gets to the body of the fish. The disease is not contagious but fish with a weak immune system easily catches the bacteria. Any fish can suffer from Fin Rot but usually, bettas and Goldfish are mostly caught in this infection.


• Poor water quality allows the bacteria to spread and invade the tank and infect the fish.
• Gram-negative bacteria containing Vibrio, Pseudomonas fluorescens, and Aeromonas are the base cause of Fin Rot disease.
• Injury at the fins or tail of the fish from a fish fight or manhandling letting the bacteria infect fish.
• Overfeeding the fish results in leftover food and more excretion of waste because fish eats more than it needs.
• Overcrowded fish tank leads to fish stress and leads to a higher risk of infection due to reduced immune system.
• Presence of aggressive fish among other species creates fights. This may damage the fins and increase the risk of infections.
• Water temperature under 25 Celsius with high ammonia and nitrate levels helps the bacteria population to increase.


Symptoms of Fin Rot include inflamed patches on the fins, faded color or discoloration on the edges of the fins, and fraying of the fin or tail. Other symptoms include lethargy and loss of appetite. If the disease is left untreated, the disease can spread to other areas of the body.

• Early symptoms appear on the top, tail and bottom fins. Find discoloring edges of the fins.
• Inflamed patches on the fins.
• Slightly severe fin rot shows brown fin edges or jagged edges. Spots in white color occur on the fins.
• Fin rots at a larger level. They recede and deteriorate. Fuzzy growth on fins and bloody edges sometimes.
• Severe fin rots cause entire fin membrane loss. The body of the fish develops cotton-like growth. Fish becomes lethargic and hardly swims.
• Loss of appetite.


• If the bacteria infection is mild, do a partial change of the water in the tank. Change 30 percent of the water.
• Add chloramine/chlorine remover first to the new water.
• In mild infection attacks, API Melafix Antibacterial Fish Remedy is helpful.

Adding some salt to the fish tank will also effective but do not use iodized salt because it is toxic to the fish. Use 1 tablespoon of salt for every 5 gallons of water. Aquarium salt inhibits the growth of bacteria and fungus.


• For treating severe Fin Rot, salt and Melafix are not enough. Use antibiotics like Maracyn.
• Tetracycline is another good antibiotic for killing both gram-negative and gram-positive bacteria and effective on fin rot disease.
• Remove the active carbon from the filter before treatment or it will remove the medicine from the water and treatment may fail.
• Better if you treat them in a separate hospital tank. Each time before adding a new dose to the water, change the entire water and replace it with clean aged or conditioned water. Continue with this until you finish the treatment.

Use gravel pipet while doing water changes to remove as much as possible of the bacteria population settled in the gravel. If the rate of infection was at a very high level all over the aquarium, after treating the tank, take out all the decorations and wash them. Also, wash the gravel and tank with hot water before refilling the tank with fresh clean water.


• Do not overcrowd the aquarium with fish of different species or even with the same species.
• Do not overfeed your fish.
• Fish that are aggressive or that nip the fins like tiger barbs should not live together with fish that have long fins like bettas or angelfish. Keep them separate.
• Partial regular water changes are good for keeping the water quality higher.
• Keep the tank clean with good filtration technique and proper filter turnover capacity.



Dropsy is also called ascites. Dropsy is a symptom that appears on fish when they are suffering from an underlying disease. The affected fish becomes extremely lazy and loses appetite. The fluid builds up in the body of the fish and it may be taken as kidney disease, due to insufficient removal of excessive and waste fluids. There are several reasons why a fish suffers from dropsy. It is difficult to find the real cause of dropsy in the fish. Dropsy is not contagious; however, the underlying cause can be contagious if it is a serious infection. But it can be fatal for the fish if the underlying cause is not diagnosed and the fish is not properly treated.


• Bacterial infection.
• Many internal bacterial infections and parasites or tumors and viruses are the reasons for dropsy.
• Bacteria Aeromonas is the most common cause of fish illness which leads to dropsy if in developed stages because of the damages on kidneys.
• Aeromonas is more pathogenic than the other bacteria. Sometimes they cause red streaks on the fish body which makes it easy to recognize the cause of dropsy.
• Regular tank cleaning and water changes are crucial to avert Aeromonas.
• Overcrowding.
• Sudden changes in the pH of water or the temperature while changing the water can affect the fish badly and may cause dropsy.


• Swollen body and protruding scales.
• The gills become pale and do not remain shiny red.
• The eyes bulge out.
• Fish is lethargic and barely swims.
• Complete loss of appetite or eating less than usual.
• Weak and feeble.
• Fish feces are stringy and pale in color.
• Fish comes near the surface more often.
• Ulcers appear on the rear half of the body in severe conditions.


• Isolate the infected fish with a swollen body in a quarantine tank for treatment.
• Consult an expert to find out the real cause of dropsy because if you treat it for a bacterial infection and the fish is suffering from a viral infection, your treatment is useless.
• Add some Epsom salt to the water. Epsom salt contains magnesium sulfate and not sodium chloride. Add only 2.5 teaspoons of Epsom salts per 40 liters of water.
• Feed the affected fish with antibacterial fish food for 7 to 10 days.
• Add Maracyn-2 to the hospital water tank. This is good for treating gram-negative bacterial infections. The fish’s skin absorbs it directly from the water.
• Observe eating pattern and social behavior of the fish; usually, the fish stops eating and does not mingle with other fish before the swelling appears on her body. Early diagnosis and treatment increase the success.


• Dropsy is very difficult to treat in fish because the real underlying cause is difficult to diagnose. That is why preventive methods are an excellent option.
• Keep the tank water clean. Change it either at least 50% once in a while or partially every week. Partial water change is easier and better to carry out and preventive.
• Do not overfeed your fish or overcrowd the aquarium.
• Keep the tank water at the right parameters. Do not let nitrate, nitrite or ammonia reach over the limits.
• Buy the right species combination for your aquarium.
• Keep the filter maintenance optimum and siphon the substrates regularly.
• Check the water temperature to avoid any sudden rise or fall.

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