Freshwater Aquarium Medications

Quick Reference Chart

For a very long time, I’ve never quarantined freshwater fish or even had to treat for any illnesses, but after a few back-to-back issues, I’ve changed my methods. Even in freshwater, it just isn’t worth the risk to bring fish into an established tank and risk something aggressive burning through your livestock faster than you can even treat for it.

The problem was that I don’t have that much experience treating diseases in freshwater. I’ve certainly encountered quite a few, but I couldn’t even remember the last time I had to use any medication. My methods of minimizing stress in the tank, feeding very high-quality food, and doing big weekly water changes were very effective at preventing any major issues. Even when something came up, it hit one or two fish, but didn’t spread like wildfire. That, along with some luck in simply not introducing anything too aggressive, worked for a very long time. On the rare occurrence when something came up, I did water changes, added salt, and hoped for the best. This worked surprisingly well.

However, after having some guppies bring in Columnaris and wipe out hundreds of dollars of fish in a 220 that wasn’t even close to fully stocked yet, I’ve changed my mind. What made it worse was that I didn’t treat with medications immediately. Generally, I do a water change and add salt. That wasn’t enough. I finally went in search of meds, but I’m limited in my immediate area to Petsmart and Petco and neither had anything that would treat Columnaris. By that point, it had peaked and the daily deaths were getting fewer and fewer. I had to settle for waiting for it to run its course.

I bought a bulk jar of erythromycin to keep on hand for any future episodes. In addition, I will be quarantining all fish in the future. Part of the quarantine will be a prophylactic treatment with erythromycin, Ich-X, and General Cure.

In researching how to treat my issues, I realized there weren’t any good articles on which medications are best for each disease.

In addition, I was reminded of the myths, misinformation, and exaggerations that surround the use of medications in aquariums.


I want to start by emphasizing how big of a role stress plays in disease. Many people think of diseases as super nasty things that will spread through your tank like wildfire with any exposure. Although there are times when this can happen, generally this couldn’t be further from the truth. It is well established that stress weakens the immune system. That weakened immune system allows whatever pathogens are around to take hold and cause an infection that wouldn’t stand a chance against a full-strength immune system. Keep in mind, there are always pathogens around. I don’t care how well you quarantine and how long it’s been since you added fish and not had any problems, if the fish get stressed enough, something will take hold and make them sick. This is why college kids get colds in May during exams. It isn’t just a coincidence that some virulent cold virus was brought to campus, it is because people are stressed, their immune systems are weakened, and that allows cold viruses (which are always around) to take hold and cause an actual illness.

Any time a fish gets sick, think about the pathogen, but think about the stressor too. If you don’t fix that, you won’t be able to fix the illness, or at best you will get rid of one illness and they will still be left vulnerable for anything else that may be around. Fix the stressor. It may be a water change that was too cold or too hot, or maybe the chemistry in the tap was too different than the tank’s because you don’t do your water changes every week which is what keeps the tank’s chemistry matching that of the tap. Maybe you have a malfunctioning heater. Maybe a fish that’s a little nippy is just too much for the other fish who have no way to get away from him even though it doesn’t look that bad. Maybe you have a nocturnal fish that you never see so you don’t think he might be aggressive, but at night he’s terrorizing the other fish. Maybe there aren’t enough decorations in the tank to help the fish feel really comfortable. Maybe you have nervous fish and your two-year-old banging on the tank is freaking them out (in this case, one of the best things you can do is to knock on the tank when you feed so that the fish learn to associate the banging with something good, the food!). Whatever it is, figure it out and fix it. Sometimes this can make all the difference in how well the fish recover from the illness (in some cases, it can be the ONLY fix needed).

Scaleless Fish

One of the most common myths is that scaleless or small-scaled fish are more sensitive to medications. The same myth is also applied to salt. The myth is wrong in both cases. I can’t tell you how many times I’ve treated loaches, pictus cats, neon tetras, silver dollars, etc. with meds that even warn against it on the label. I’m guessing the label is either there because of the myth (these products aren’t regulated in any way, so there’s no “official” directions or warnings for any of them) or a disclaimer for the company so that in the rare instance where there is an issue, you can’t get too mad at them. What’s even more confusing is that this myth is applied to thick-scaled fish such as cories and plecoes. If scales had anything to do with it, these fish would be extra tolerant of these meds, not sensitive to them.

Using Multiple Medications Simultaneously

Another myth is that you can’t use two different meds at the same time. This is only true if they have the same active ingredient. If two different meds have methylene blue, then dosing both properly will result in a methylene blue overdose (which may or may not even be harmful). In fact, some meds are already combined (such as Ich-X, Furan-2, and General Cure) and others can be even more effective when used in conjunction (such as Melafix and Pimafix). So double-check the label, but don’t hesitate to use multiple medications at the same time, especially when you aren’t sure what the problem is (such as dropsy).

This isn’t to say that it’s impossible for you to have a situation where a fish reacts poorly to a medication. Maybe it’s because it’s a scaleless fish, but maybe that individual is just so far progressed in the disease that it’s already too weak. Remember, these medications aren’t usually easy on the fish and the medication itself, even when properly dosed, can be a stressor for the fish, especially a fish that’s already weakened by disease.

Identification (Why No Pictures?)

Although I would love for this article to be very extensive and everything you ever need to know about diseases and medications, it isn’t. There are some things I just can’t properly cover here, so I won’t try. For example, if you really want to, you can get into all sorts of details about the biology of each pathogen, how long they can remain dormant in an aquarium, their different life stages, etc. This article isn’t about that, it’s meant to be a quick reference to help you begin effective treatment as fast as possible.

In addition, for exact identification, even if I had a couple of good pictures of each disease (which I don’t ), your case may look different and that could lead to false identification and ineffective treatment. For that reason, I recommend you simply do a Google Images search for the symptoms and disease names so that you can see lots of examples. If you are still in doubt, email me or post a picture on a forum.

Hospital Tanks

You may find the use of a hospital tank (sometimes inaccurately referred to as a quarantine tank) recommended when treating diseases, and it may seem like the safest way to treat the infected fish while protecting the others, but it isn’t. If there is a disease in the display, it’s in the display tank and every fish in the display has been exposed. Removing the fish from the display to treat it separately causes completely unnecessary stress to that fish and leaves the problem unaddressed in the display. At best, this means the disease may remain dormant to potentially cause a problem in the future, but at worst it can mean other fish will start getting sick. Unless you have a really good reason to separate a fish (such a the sick fish can handle a certain medication, but you have another species in the display that truly can’t), treat the display.

Carbon Filtration

Almost all medications require you to remove carbon media from your filtration because otherwise the carbon will quickly remove the medication. I don’t recommend the constant use of carbon anyway, but if you are using carbon, definitely remove it before starting any medication.

Once treatment is complete, you can add carbon to remove the medications. I usually just do a couple of extra water changes to remove the medication. Water changes are good anyway, but since my water changes are so large (usually 75-90% in most of my freshwater tanks), it is also very effective at removing medications. If you are doing smaller water changes, the use of carbon would be better (but you may also want to consider stepping up to larger water changes). For more information about water changes, please read the article on Water Changes and Water Quality.


Ich is one of the most common diseases in freshwater. It is so common that many if not most aquarists deal with it within a couple of months of getting into the hobby. The good news is that it is also pretty easy to deal with as well. If you have any doubt about whether it’s ich, it probably is. Ich looks like someone salted your fish, it literally looks like grains of table salt stuck to your fish. It is so easy to treat that some people don’t even use meds, favoring water changes, salt, and a raised temperature instead. I have found that in some cases the only change needed is to simply remove whatever is stressing the fish which is what is allowing the ich to cause an infection in the first place. For more information, please read the article on Treating Ich.

Medication: Ich-X

Hole in the Head

Hole in the Head and Head and Lateral Line Erosion are two distinct illnesses. I have whole article on them with more detail, but Hole in the Head found in angels, discus, etc. is caused by parasites. The holes are limited to the head area where the holes are usually narrow and deep and often have a white discharge. Sometimes there is so much discharge that you don’t even see the holes, which leads many people to conclude “It’s obviously not hole in the head if there are no holes!”, but they’re wrong. For more information, please read the article Hole in the Head (HITH) and Head and Lateral Line Erosion (HLLE).

Medication: Metro+ (or anything else containing metronidazole).

Quick Reference Chart

A note about the Notes column: many medications specifically say things such as “not safe for invertebrates or plants”, “use a half dose for scaleless and small-scaled fish”, etc. The Notes column may not agree with those labels. I’m not sure if the labels are just being extra cautious so that no one who loses fish can then blame the company, but I have had a lot of personal experience showing that these precautions are rarely accurate. In addition, in my research when I had my 220-gallon community tank break out in Columnaris, one of the best resources I found was Aquarium Co-Op where he explicitly states that they have never had issues with plants, inverts, or the nitrifying bacteria with the various medications he recommends. This is exactly the type of experience I find most valuable and it lets me know to go ahead and treat with the best medication. So although it is possible that you may experience a complication when using one of these medications, please know that is very rare (but there are always exceptions), and even then it can be hard to determine whether it was the medication that was truly to blame or if the fish was already too sick or stressed, or perhaps that whatever caused the stress that allowed the disease to break out in the first place may have an impact on tank inhabitants that didn’t show in obvious ways. I also think it’s best to treat aggressively as soon as you see a sign of a problem, don’t wait because you aren’t sure how every single inhabitant may handle the treatment.

These aren’t the only medications I would use or recommend, these are popular ones. If you can’t find these exact medications, pay attention to the active ingredients and look for other medications that contain that active ingredient. For example, erythromycin is in both E.M. Erythromycin by API and Maracyn by Mardel. So if you can’t find E.M. Erythromycin, don’t hesitate to buy Maracyn just because it’s not the example I use in the chart.

Active Ingredient
General Cure
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Metronidazole, PraziquantelParasitesInternal parasites, hole in the head, fish lice, flukes, velvetInvert Safe
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MetronidazoleHole in the HeadFor use in hole in the head in discus, angelfish, rams, etc. (Hexamita spp. and Spironucleus vortens)Invert Safe
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Nitrofurazone, Furazolidone, Methylene Blue BacteriaGram-positive and gram-negative including Columnaris Will harm nitrifying bacteria
E.M. Erythromycin Erythromycin BacteriaColumnaris, body slime, fin and tail rot, mouth rot, open lesions, septicemia, popeye Invert safe, nitrifying bacteria safe
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Formaldehyde, Methanol, Malachite Green Ich and FungusFreshwater ich, marine white spotInvert safe
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KanamycinBacteria and FungusColumnaris, popeye, fin rot, septicemia, dropsy, mouth rot Invert safe
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A natural tree oil Bacteria, Accelerates Healing Broad-spectrum for bacteria when the medications listed above aren’t an option Invert safe, plant safe, reef safe, nitrifying bacteria safe
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A natural tree oil Fungus and Bacteria Broad-spectrum for fungus when the medications listed above aren’t an optionInvert safe, safe for nitrifying bacteria