Bacteria and Antibiotics in the Aquarium

Polyp Coral

Friendly bacteria include the scavenging, decomposing bacteria digesting uneaten fish food, plant matter, dead algae, and basically everything that consist of organic matter.

The nitrifying bacteria aka nitrifiers aka beneficial bacteria, convert ammonia (resulting from bacterial activity, fish waste etc.) into the less toxic compounds of nitrite and nitrate. On rare occasions, denitrifying bacteria can settle in oxygen free areas and transform nitrate into oxygen and nitrogen gas.

‘Unfriendly’ bacteria are summarized as pathogenic, disease causing bacteria.

Pathogenic bacteria are opportunistic, meaning as long as the fish is healthy, it will not be bothered. Some bacteria are present at all times and in a constant fight with the fishs’ immune system. A strong immune system allows the survival of the bacteria strain without harming the fish.

Bacterial infections are secondary diseases, they can only prevail if the fish is weakened under stressful conditions (heat, ammonia, nitrite, high organics, low dissolved oxygen etc.), resulting in rapidly multiplying pathogens.

A stressed and weak fish with pathogenic bacteria present results in a bacterial infection, which will be fatal if left untreated. A bacterial infection can therefore be defined as by pathogens outgrowing the defending cells of the immune system.

Any time a bacterial disease occurs adjustments in the aquatic environment need to be made in order to lessen and to eliminate stress causing factors to the fish. Bacterial diseases should be treated with antibiotics, preferably in a quarantine/hospital tank.

Antibiotics function by slowing down the pathogens thus increasing the immune systems efficiency. Nevertheless, it is the immune system that cures the disease not the antibiotic.

To achieve a slowdown, antibiotics interfere with the reproductive mechanisms of the pathogen by interrupting its lifecycle.

The two relating terms are antibiotics and antibacterial. While antibiotics are naturally produced by a microorganism to kill another microorganism, antibacterial substances such as sulfa and furans are manufactured artificially. (The term antibiotic is further used in this text referring to both, antibiotic and antibacterial).

To apply the correct antibiotic to a given pathogen the pathogens cell wall is decisive for the determination. Pathogens have either a thin or a thick cell wall.

The method to differentiate between the two main types of bacterial cell walls is called the “Gram Staining Technique”. Developed by the Danish physician Hans Christian Gram, Gram stained bacteria samples with the coloring agent crystal violet then applied potassium iodide resulting in a water insoluble blue-purple discoloration of the bacteria. Adding ethanol-alcohol as a decolorizing compound, the bacteria either retained the blue-purple color or turned red following a treatment with Safranin a counter-stain used for visibility purposes.

The blue-purple color indicates a thick cell wall and is called “gram positive”, while red indicates a thin cell wall and is referred to as “gram negative”.

This is of importance because of the response towards certain antibiotics.

Antibiotics against (thick wall) gram positive pathogens prevent the build up and repair of the cell wall whicheventually will lead to the cell content leaching out, consequently killing the pathogen. Antibiotics against (thin wall) gram negative attack by interfering with the protein synthesis (metabolic process) therefore eliminating the cells ability to produce food.

Gram positive antibiotics will not have any effect on gram negative bacteria nor will gram negative antibiotics have an effect on gram positive bacteria.

The most common pathogen in the aquarium are the aeromonad species for freshwater and its counterpart vibrionaceae in marine and reefs. Both are gram negative and everywhere present in the aquarium as part of the bacterial flora.

Aeromonads/vibrionaceae can be responsible for dropsy, abdominal swellings, skin ulcers, red patches, fin and tail rot and pop-eye.

General indicators of bacterial diseases can be disformed frayed fins, open sores, red steaks on fins or along the fish body, grey film on eyes, swollen or bloated belly, lethargic behavior, loss of appetite to name a few.

Antibiotics for use in the aquarium come in all forms and shapes – liquid, powder, or tablets.

It is essential to determine the disease causing bacteria in order to apply the correct antibiotic. The application dosage and time frame should be followed according to manufacturer’s recommendations.

Some common antibiotics used in aquariums

  • Erythromycin which treats gram positive bacteria and is best used in an alkaline environment (pH of 7 and up).
  • Aminoglycosides marketed as neomycin, kanamycin and streptomycin are active against gram negative bacteria and work well in alkaline water conditions.
  • Sulfonamide known as sulfa or triple sulfa have antibacterial characteristics inhibiting the growth of bacteria. An alkaline environment is preferred and sulfonamide as well as aminoglycosides can be used in marine environments.
  • Nitrofurans (furane, nitrofurazone) are also antibacterial but will loose their potency with increasing pH levels. They are therefore preferred freshwater treatments as is the tetracycline group.
  • Tetracycline is bacteriostatic, inhibiting protein synthesis. This drug will get less effective in hard waters as it readily binds with calcium and magnesium.
  • Quinolones, antibacterial to treat gram negative bacteria, prevents DNA synthesis and can be used in a broad pH spectrum.

Bacterial diseases in fish can face antibiotic resistance, which means that the bacteria strain has mutated leaving it unaffected by the antibiotic. Another antibiotic will have to be used should this occur.

Bacterial diseases are not contagious and infected fish should be treated separately in a well aerated hospital tank. Antibiotics are potent by themselves and never meant to be used in combination, as some of them can eliminate each other or create toxic effects for fish.

Keep in mind that the beneficial bacteria are gram negative as well.

Leave a Reply

11 Comment threads
12 Thread replies
Most reacted comment
Hottest comment thread
15 Comment authors
Notify of

I have a betta fish that’s had torn fins so I added antibiotics (bettafix) to the water. I’m curious to whether or not I can also add a dechlorinating agent as a water conditioner. Will the combination have toxic effects on the fish?


There is no interaction between a water conditioner and antibiotics. Water conditioners to remove chlorine are essential for the well being of the fish.

Jennifer Arbuckle

I just treated my 33 gallon aquarium that is home to two very large black goldfish as well as 3 other fish that I’m not sure what they are and a sucker fish for a bacterial infection did everything the package said I removed the carbon filters cleaned the filter very well no soap and have the filter running (aeration) well there is white foam on the surface of the water should I be concerned?


High surface tension or protein concentration. Take a paper towel, hold it on two corners, and slide it over the surface to remove the foam.


I have dlowron fish . Ther is white lauer on fish eye from few days amd I yhink fish is not able to see anything. Pls suggest


Hi, I have a red fin shark that has an extremely distended stomach to the point that his scales are busted. I’ve been looking online and think it may be dropsy?? Has anyone ever delt with this or knows what I should do???

Sorry to hear about your shark. It’s always best to talk to someone at a fish store with knowledgable staff. They should be able to help diagnose the disease and recommend a treatment. Sorry we can’t be of better help here online.

Nina Fisher

The gills of my angelfish are actually rotting out. I have lost one already and I see another has the same problem. What can I do?

First thing to do is set up a quarantine tank if you’re able to. The sick fish should be separated from healthy fish immediately. Then you should visit your local aquarium store asap. Explain the problem so they may help diagnose the illness and recommend a treatment solution. Your pet store is always the best first stop when dealing with fish health problems. They can send you home with the appropriate medication after successful diagnosis.


My beta has cloudy/puffy eye on the left. I want to treat in 2g bowl. I have TETRACYCLINE. How much of a packet to use in bowl? The directions say use whole packet for 10g.

Please always follow the directions on the package of the medication. Any questions for a specific product should be directed to the manufacturer.


Must i change water after antibiotic treatment as i use MR. YELLOW and it changed the water color to yellow. Please Suggest

Always follow the product manufacturer’s instructions and recommendations. Changing the activated carbon is always a good idea after medicating and treating any aquarium. Carbon is used for chemical aquarium filtration and will remove many medications and other chemical impurities.

Turtle lover

Hello just wondering does aqaurium salt have ampicillin? My betta developed popeyes recently and i gave him aquarium salt baths. Pls reply asap thks


No aquarium salt does not contain any antibiotics.


I started my goldfish on doxycycline for cloudy eye and it says on the directions to remove the carbon filter which I did. My filter also has a smaller ammonia filter. Should that be removed as well??

Please contact the manufacturer of the medication. They should be able to answer any questions about their products you may have.


Hi – a couple of things. You had said that “it is the immune system that cures the disease not the antibiotic.” It’s actually the antibiotic, which is easily proven by putting bacteria and an antibiotic in a petri dish. The bacteria will all be killed with no immune system present… hence the antibiotics cure it, not the immune system. Okay sorry to give you a hard time on a pretty good article 🙂 Next, all of your data focuses on Gram-negative and Gram-positive antibiotics, but you didn’t mention the most important of all, the broad-spectrum antibiotics. Cephalexin (sold as… Read more »


Your addition to the article is greatly appreciated.


Just to add though certain antibiotics are bacteriostatics; which rather than killing the bacteria they inhibit bacterial growth which allows for the organisms own immune system to combat the illness. There are a lot of antibiotics in this category such as Nitrofurantoin or erythromycin. Amoxicillin targets the bacteria directly and is not a bacteriostatic.


I’m hoping that seaplex is another broad spectrum antibiotic as I’m treating my angels for what appears to be mouth rot with that product

Ashish Kalia

Can we use directly in aquarium this type of antibiotic when fish in aquarium

Always follow the manufacturer’s instructions and recommendations for any medication used in the aquarium.

Click to Hide Advanced Floating Content
Cart Menu Button Image0
Your Cart