Aquariums 101: Fish Disease Diagnosis + Treatment


Aquariums 101: Fish Disease Diagnosis + Treatment

Anyone who keeps pets will have to deal with diseases. And given the tight conditions and poor water quality that beginning aquarists sometimes run into, fish are inevitably going to get sick. So how can we diagnose diseases as early as possible? And when we have, how do we treat them?

Signs of Disease Stress in Aquarium Fish

Recognizing signs of aquarium fish disease can help you diagnose and treat issues before they become serious. Here are a few easy ways to do so!

Eye, Gill, and Mouth Issues

Some of the first places you should examine are the eyes, gills, and mouths of your fish. Discoloration, wounds, and other dangerous infections often show up here. Bettas, for example, are susceptible to infections around the eyes, which will bulge from accumulated fluid.

Many fish can also get mouth fungus, which manifests as cottony growths coming from their mouth. Subtle discoloration around the mouth and a loss of appetite are often a sign of columnaris, a common infectious bacteria.

Skin and Fin Issues

The skin and gills of your fish also contain clues to their health. Color loss is an easy sign to look out for. When the aquarium lights first come on your fish will look washed out but they should perk up as the day goes on. Constantly faded colors are usually a sign of stress from cold, aggression from tank mates, water conditions, or disease.

The scales of the skin should be clear. If you suddenly see a bunch of missing scales you should try to determine if an aggressive tank mate was the cause. But also watch out for diseases since scales are like armor, preventing germs from penetrating into the skin. Many parasites are also obvious if they infect the skin, such as Ich or Anchor Worms.

Fish fins are a common place for issues to arise because they are so delicate in many species. Long-finned fish like Bettas and Guppies are especially likely to develop issues when their fins are damaged by fights with tank mates or catching on decorations.

If you see frayed or split fins you don’t need to be worried right away. So long as the water conditions are clean and your fish are healthy their fins will recover mostly to entirely. It’s when bacterial and fungal spores are all over the tank due to unsanitary conditions that diseases take hold here.

Clamped fins are another sign. Fish hold their fins close against their body to minimize their profile. Or they may simply not have the energy to spread them fully. This is usually a sign of general stress – it’s not always due to disease. It’s just a sign that you need to check in and figure out what’s up.

Behavioral Cues

The third clue is to know the normal behavior of your fish. And all this takes is being observant and knowing how your fish normally behave. If a normally active, eager eater is refusing food, be curious as to why before it starts losing weight and starving. If a previously healthy fish is suddenly spending all of their time hiding, check on them to ensure all is well.

When fish get sick they may start laying along the bottom of the tank. Or they may stay close to the surface instead. Wobbly swim patterns, suddenly shimmying out of control, lack of interest in their own kind, listlessness, and other behavioral changes can all be clues that point to a disease problem.

Common Aquarium Fish Diseases

There are dozens, if not hundreds of different fish diseases out there. But these are some of the most commonly encountered disorders to deal with in aquarium fish!

Ich (Ichthyosporidium/Cryptocaryon irritans)

Ich is one of the most common fish diseases that people encounter. It’s almost like the flu for fish; highly contagious but rarely fatal. Unlike the flu, ich is caused by a parasite that lives on the skin. It manifests as little white dots about the size of a grain of salt. These dots eventually burst as the parasite grows, releasing spores into the water that spread to your other fish.

Ich infections are very common in heavily stocked aquariums and systems that share water across a sump – such as pet store aquariums. Diseases like ich are why you never want to pour pet store water into your home aquarium; you’re just asking for an infection that way.

While ich is rarely fatal, it can be persistent and dangerous if allowed to continue infecting fish for a long time. It is especially hard to treat and dangerous to fish with small scales, like Neon Tetras.

Scaleless fish like Clown Loacheshave an even harder time with ich because they are sensitive to the medication dose as well. An anti parasite remedy plus moving a fish to a quarantine tank at the first sign of the disease is your best strategy for beating it!

  • Cause: Ichthyosporidium/Cryptocaryon irritans (crustacean skin parasite)
  • Danger Level: Low
  • Contagious: Very
  • Treatment: Medication, Quarantine
Fin and Body Fungus

Fin and body fungus are topical diseases that most aquarists have to deal with eventually. They manifest as a cottony white growth covering open wounds or damaged fins. Fungal infections are often confused with bacterial infections. And since fungal medications don’t work on bacteria and vice versa, it’s worth making sure you know what you are dealing with.

Fin and body fungus almost always require an open wound to grow from. Bacteria don’t always need one. And the cottony clear or white growth extending from the wound is a sure sign you’re looking at fungus.

Fin and body fungus are caused by the same agent: opportunistic fungi that are found in all aquariums. Normally these fungi are content to feed on items like leftover fish food and feces. You may see cottony growth over decaying organic matter; that’s the exact same fungi in action!

That’s why fin and body fungus isn’t contagious in the usual sense; fungal spores are everywhere, even in healthy tanks. But if you see a fish infected by it, it means that their immune system can’t keep up with how many spores are in the water.

Dirty aquariums high in ammonia and other nitrogenous waste simultaneously depress fish immune systems while providing plenty of organic waste for fungi to grow in.

Medication and water changes are the best ways to treat fungal infections in fish! Test the ammonia, nitrite, and nitrate levels. They are bound to be elevated and in need of reduction. You may also want to quarantine an especially sick fish but it’s not necessary since the spores are already everywhere in the main tank.

  • Cause: Fungal spores
  • Danger Level: Moderate
  • Contagious: No
  • Treatment: Medication, Water Changes
Bacterial Infections

Bacterial infections are very similar to fungal infections in many respects. They share a cause: dirty aquarium conditions. Leftover food, feces, and other organic matter causes bacterial populations to explode. And once the immune system of your fish begins to falter under the constant assault, bacteria can set up shop in their bodies.

Unlike fungi bacteria don’t always need an open wound but they do help. A bacterial infection is also very variable in appearance. It can look like a thick, slimy patch on the skin, a cloudy eye, discoloration around the mouth and gills…Or more commonly, bright red blood vessels and patches on the skin (Aeromonas bacteria). Fish may show wounds, start scratching against tank decorations, sit at the bottom, and refuse to eat.

Once you see signs of a bacterial infection it’s usually the case that your water conditions are too dirty and need attention. You’ll also need to use an antibacterial agent to help your fish heal from the germ overload. Fortunately most fish recover quickly, assuming you don’t wait for the infection to progress too far.

  • Cause: Bacterial spores (Columnaris, Vibrio, Aeromonas, etc)
  • Danger Level: Low to Moderate
  • Contagious: No
  • Treatment: Medication; Water Changes
Internal Organ Disorders

These go by several names since they are caused by several agents and affect several organs. Many internal organ disorders are also caused by bacterial infections. Usually germs somehow get inside – or germs that are normally harmless become a problem and start multiplying.

One of the most common to see is Dropsy, where bodily fluids accumulate in the abdomen. Fish with Dropsy become so swollen that their scales extend outwards, like a pinecone. Their eyes may even begin to bulge from the fluid pressure. Dropsy is usually fatal but fortunately not contagious.

Swim bladder disorders are another organ failure caused by out of control bacteria. In this example your fish lose the ability to control their buoyancy normally and start floating along the surface helplessly.

The third most common are intestinal disorders. These manifest as bloating without your fish floating or the scales protruding. Most of these are caused by intestinal bacteria getting out of control. Fish food of the wrong type can cause this, as can feeding pond fish heavily in the fall and winter.

Their digestive system has slowed down due to the cold and can’t process food fast enough, which allows bacteria to begin rotting it within them. That’s why stores sell special cold water pond blends, which are mostly easily digested wheat germ!

  • Cause: Usually bacterial
  • Danger Level: High
  • Contagious: No
  • Treatment: Medication; Water Changes; Food Changes
Anchor Worms

Anchor worms aren’t super common in tropical fish but they aren’t unheard of. They are much more commonly found in goldfish and other outdoor pond fish. Occasionally they find their way into aquarium systems, though. Especially if you offer feeder fish to Oscars and other predators, which can carry anchor worms.

These skin parasites look like short, stringy white worms trailing from the skin and gills. However they are actually a parasitic crustacean (a copepod)! They bury their head under the skin to feed on blood. The trailing parts are the external body and eggs that are released into the water column to infect new fish.

Anchor worms are rarely fatal but they do sap blood, look unsightly, and are very contagious. The wounds they also leave behind don’t always heal completely, leaving scars on your fish. Fortunately, treatment is straightforward.

The first thing to do is to diagnose them and then catch the infected fish. You’ll want to hold them down in a wet towel, net, a wet hand, or other covering. Never touch a fish with dry skin because you will strip away their slime coat, which prevents infections.

Using tweezers you should grasp the anchor worm at the base firmly and slowly pull it free of your fish. This process is best saved for larger fish because a small piece of flash may be removed with the worm. A small fish can be too traumatized by this to survive.

After the worms have been removed treat the entire tank with a copper-based anti parasite remedy to kill the eggs, larvae, and any adults you may have missed.

  • Cause: Skin Parasites
  • Danger Level: Low
  • Contagious: Yes
  • Treatment: Physical Removal, Medication
Head and Lateral Line Disease (Hole in the Head)

This disease is actually very specific to marine Tangs and Surgeonfish. But it is very commonly seen in marine aquariums because few folks understand the needs of these fish, which leads to many unnecessary deaths.

The disorder goes by Head and Lateral Line Disease or Hole in the Head Disease. Tangs with this issue will show gaping pits in the flesh around their face. The skin often starts to lose color, fading to grey or white. And similar pits and color loss show up along the lateral line, a skin organ fish have to sense changes in pressure and current.

While gruesome looking, the cause is actually very simple. Tangs and Surgeonfish are vegetarians and require a diverse diet full of greenery. Feeding these fish standard aquarium food, which are mostly cheap starch, protein,and fillers, is a recipe for failure. It’s sort of like scurvy in humans.

Fresh seaweed, macroalgae, and even terrestrial greens like blanched spinach and zucchini all provide these fish with the vitamins and minerals they need. Head and Lateral Line Disease can become too advanced to recover from but it is reversible if caught early enough.

  • Cause: Nutritional Disorder
  • Danger Level: High
  • Contagious: No
  • Treatment: Change in Diet

Medications to Keep on Hand

Once you’ve diagnosed the disease then it’s time to treat it. Keep in mind that these are just a sampling of what’s out there. And whenever you use a medication be sure to follow the instructions very carefully. Perform water changes as needed and dose the exact amount as specified by the instructions!

Antibacterial Remedies

The hardest part of treating bacterial diseases is identifying which germ is the problem. There are several common varieties that cause diseases so using a broad spectrum antibiotic is the easiest approach.

If you can specifically identify which bacteria are causing the infection then it is possible to target them with precisely the right antibiotic. Whenever possible it’s good to do this since broad spectrum antibiotics can also eliminate many beneficial microorganisms in your aquarium.

Some may even kill the nitrifying bacteria that process ammonia into nitrite and nitrite into nitrate. When this happens you’ve just reset the cycling process of your tank, which can lead to even bigger problems for your fish!

If you can’t determine which germ is the problem then move any infected fish to a separate quarantine tank. This way any medications you use won’t cause harm to your other animals or filter bacteria.

Broad Spectrum Antibacterial Remedy

A general antibiotic is always helpful to have on hand, especially one formulated to target infectious bacteria. Melafix is ideal for this reason: it leaves the beneficial nitrifying bacteria alone and targets most disease-causing types! This formula is safe to use both in your main and quarantine tank.

Antifungal Agents

Antifungal remedies are much more straightforward. Most species will respond to a single formula and there aren’t so many beneficial fungi to worry about in the average aquarium. They will gradually recover and form a healthy ecosystem post-treatment.

You can also simultaneously dose antibacterial and antifungal remedies if you aren’t entirely sure which you are looking at. Just be careful when treating scaleless fish like loaches, eels, and catfish.

These fish tend to soak up medications at higher levels than fish with scales because scales act as a barrier, slowing down uptake from the water column. If your scaleless fish absorbs too much too quickly it can sometimes be fatal – dose at ½ to 3/4ths the usual amount, increasing only if you see no signs of improvement after a few days.

Aquarium salt and raising the water temperature can also help fish recover from fungal infections.

Anti Parasite Medications

The nice thing about parasitic infections is that they typically respond very well to medications. If you can add a bit of aquarium salt and raise the water temperature a little to boost the immune system of your fish, that can also help speed recovery!

One warning: never use anti parasite remedies if you have snails, shrimp, crabs, and other invertebrates in your tank. Treat diseased fish in a quarantine tank – or move your invertebrates to a new tank for a few days during treatment.

Anti parasite medicines often kill ALL invertebrates. Many use copper based formulas, which all invertebrates are sensitive to. Other formulas include agents like methylene blue and malachite green, which have been staple remedies for decades. They tend to stain the water for a few hours but the effect is harmless.

Even if the label says snail and shrimp-safe, I would be very cautious because these animals vary in sensitivity across species. What may be safe for one species can still be fatal for another.

Aquarium Salt as a Therapeutic Agent

Aquarium salt is sometimes forgotten by freshwater hobbyists. For marine fish keepers the uses are obvious. But it actually has a place in freshwater systems as well!

Salt acts as an ion regulator, helping the gills of fish more easily exchange ions (charged elemental atoms) from the body into and from the surrounding environment. All but the most extremely pure freshwater bodies of water have all kinds of dissolved salts.

NaCl (sodium chloride) is a general tonic, boosting gill function and stimulating slime coat production. The slime coat acts as an initial barrier against bacteria and parasites, preventing them from making contact with the skin. Some parasites are also highly intolerant of salt – salt baths can sometimes be used to treat these diseases in freshwater fish!

Just be careful when dosing aquarium salt because like any mineral it doesn’t disappear with water evaporation. When topping off water that’s evaporated from your system do not add aquarium salt to it. Any salt you’ve previously added is still there and will only leave the system when you perform water changes.

One rounded tablespoon per 5 gallons of water is enough for a general tonic. If you instead want to use it as a bath to treat external parasites like Ich or Anchor Worms then a preparation of warm aquarium water with 2 ½ cups per 10 gallons of water, scaled down as necessary, is sufficient. Bathe the fish for 5 to 10 minutes, no longer, and then return it to the aquarium. You can repeat this process every 24 hours.

Aquarium plants can be sensitive to salt so be very careful not to go beyond the above dosage recommendations when using it as a general tonic. The same goes for fish with specialized scales, like Corydoras, scaleless, and small scaled fish.

Many fish, such as Livebarers and African Cichlids, actually prefer more salt! Some, such as Mollies, can even live in full saltwater conditions, where they tend to be hardier versus in freshwater tanks.

Disease Prevention Strategies

If you have no other choice, then treating diseases with medication is the only thing that may save your fish. But prevention is always the best medicine. So how can we ensure that we rarely have to deal with diseases in the first place?

Quarantining New Fish

One of the easiest ways to prevent diseases from entering your tank is to set up a separate quarantine tank for new arrivals. This is much more common in the saltwater hobby, where one infectious fish or coral can devastate thousands of dollars of livestock. So it’s an even smarter investment here.

That said, a quarantine tank need not be extravagant or expensive. All that’s required is a heated tank with a simple filter and bare bottom (for easy cleaning). A few plastic plants and other decorations will help the fish feel safe enough not to hide continually and allow you to observe its health more easily.

Sometimes wounds, parasites, and other issues that weren’t obvious at the store may become apparent once you bring a fish home. Wild-caught fish should always be quarantined because they almost always have loads of internal parasites that need to be treated with medication.

Weaning wild-caught or picky fish onto your food of choice is also a lot easier to do when they don’t have to fight with your established fish for food. A new fish may be too intimidated to feed alongside their tank mates and can slowly starve.

Another reason why quarantine tanks are so helpful is that any medications you use remain isolated! This way you can use a full or even extra-heavy dose of medicine in the quarantine tank without harming your other fish, invertebrates, or beneficial filter bacteria. The temperature and salt levels can be safely elevated as well.

Lastly, any diseases remain quarantined inside as well. This is perfect when dealing with the early stages of infectious diseases like ich, preventing other fish from having to be treated or dying from it.

Dietary Strategies

As in humans, offering a diverse diet is one of the best ways to keep your fish healthy. Food is medicine and the more vitamins, minerals, fats, protein, and carbs your fish have access to, the better.

For convenience sake you can use a prepared pellet or flake formula to form the base of your fish’s diet. But one should never only feed a prepared blend unless it’s one loaded with fresh ingredients – which tend to be pricier but very worth the cost!

Alongside your pellets or flakes you want to offer frozen, live, and fresh items like brine shrimp, blood worms, daphnia, tubifex worms, etc. These will provide missing nutrients for your fish. If your fish are vegetarian or omnivorous then you need to be offering them greens as well.

Algae, nori (dried Japanese seaweed), macroalgae, soft aquarium plants like Cabomba and Elodea, and blanched terrestrial vegetables like peas, spinach, squash, and lettuce all offer the roughage and nutrients these fish need!

And believe it or not, garlic is just as healthy for fish as it is for us! The active ingredients are antibacterial and antiviral agents. Fish food can be soaked in garlic extract, which not only helps treat internal disorders but also enhances the scent and flavor of food for picky eaters.

When trying to entice a new fish to eat you can both treat it for internal disorders and stimulate its appetite all at once with garlic!

Monitoring Water Quality

Keeping up with water quality is another way to keep diseases at bay. Many diseases, especially bacteria and fungal ones, are opportunistic. They are always around but when the water conditions grow bad they have a chance to infect your fish.

High levels of ammonia, nitrite, nitrate cause severe stress to the internal balance of your pets. When this happens their immune systems have a hard time working effectively. Plus, germs thrive in dirty conditions, taxing their immune system even further. So when you see bacterial and fungal infections arising it’s almost always because your water quality has plummeted.

Fortunately, treating poor water conditions is very easy to do. Simply perform water changes as needed. If you’ve been lax in maintaining your filter then change the activated carbon and floss as well to ensure your good bacteria can fully process accumulated nitrogenous waste products!

Temperature Control

Fish are cold-blooded animals. This means that their metabolisms are regulated by the environment. In warm conditions they eat more, move more, and grow faster. And in cold conditions it’s the exact opposite.

For Goldfish, Koi, and other coldwater fish, this isn’t really an issue. But if you keep tropical species then you need to be careful, keeping the temperature within a precise band of conditions.

The exact parameters depend on what species you’re keeping. Danios and other Cyprinids can be kept anywhere from 65-75℉. Livebearers prefer 70-80℉. Equatorial species like Discus can be stressed if the water gets much cooler than 78℉!

If you have a sick fish you can sometimes speed recovery by raising the water temperature by 3-5℉. Though make sure you’re also performing water changes and using medication as needed!

Choosing Healthy Aquarium Fish

Another solid strategy to keep your fish safe is choosing healthy fish to begin with! Pet store environments, even the cleaner stores, are places diseases tend to thrive. High animal turnover, interconnected tank systems, overcrowded aquariums, stress in newly arriving fish…All of these conditions make it easy for disease to find new hosts to infect.

So choosing disease-free fish goes a long way in keeping your current pets secure. You should use the strategies I listed in the Signs of Disease Stress in Aquarium Fish section with a bit of modification!

For starters, faded colors aren’t always a bad sign with fish in the store. They may be in a tank with few or no decorations or feeling constant stress from bright lights or tank mates. They may also not display certain natural behaviors in these strange conditions so you need to make allowances for that.

New arrivals may also refuse to eat in the beginning, especially if they are wild-caught since they’ve never seen flakes or pellets before!

Avoiding Overcrowding

Overcrowded aquariums make it very easy for diseases to spread. For one, you’re increasing the load placed on your filter and other life support systems. Ammonia and other noxious chemicals can easily spiral out of control in a crowded tank.

More fish also means more hosts for germs to infect. Within just a few days you can go from one fish with ich to several to all of your fish needing treatment. Fewer available hosts for a disease means transmission is harder – another reason why quarantining works so well.


Fish diseases are something we all have to deal with sooner or later. As I’ve demonstrated they range from minor to severe, depending on the source and how quickly you catch them. So long as you have some basic medications on hand and the knowledge to identify what the issues are, you’re already halfway to nursing your fish back to full health!


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