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So about two weeks ago I bought a betta from a lfs. Upon getting home I realized it had pop eye ( I assumed so because the eye was cloudy and popping out). I immediately started treating him with maracyn two. The eye still looks the same and idk what's wrong. Also does the water need to be circulating while I'm medicating it?
 

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How to Treat Popeye in Betta Fish
If the cause of Popeye is a mycobacterial infection, you should go ahead and first treat the root of the bacteria itself. This is easily done by cleaning the tank water and ensuring that the pH balance of the water is just slightly acidic. On a side note, nearly all bacterial infections found in bettas and other fish that are pets can be prevented or in the very least you can reduce the risk of them by doing keeping the water clean and monitoring the pH balance.
Additionally, you can treat the water with Tetracycline or Terramycin, two very popular antibacterial medications that you can purchase at your local pet store. The standard is to add this in the water...100 mg of the antibiotic for every 4 oz. of food.
If this doesn't work, you can try these other methods for a quick fix that also work well as a preventative measure for your betta...

Warm the water to 86 degrees. You will want to do this gradually at a rate of 1 degree per hour. The water temperature should already be in the high 70 degree range.
Add a little salt to the water- The key is "little". Don't give your betta fish a salt bath. The percentage of salt added to the water should be no higher than .6%

Both of these quick fixes will help to keep bacterial infections at bay. It is important to note that if your fix is exhibiting signs of Popeye, you should avoid contact. Although it is unlikely your betta has tuberculosis, it is transmissible to humans through open sores.
In conclusion, Popeye is treatable and like most bacterial infections, the cause is normally dirty water or a low pH. The best way to prevent Popeye is to make sure your betta fish is in a stress free environment. That means clean water, good food, and nice warm water.

Article Source: http://EzineArticles.com/1100151
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After the Maracyn 2 treatment is finished, I would do a water change.

Then, put a small amount of tank water in a cup. Stir in 1.5 teaspoons Epsom salt (magnesium sulfate), until the salt is completely dissolved. Slowly add this to the tank over the course of 1 hour.

The Epsom salt may help reduce any fluid retention in the eye. If it's not better after 1-2 days, I would consider getting a gram positive antibiotic, such as Maracyn (erithromycin).

Maracyn 2 contains minocycline, which is good for gram negative issues, such as fin rot. Maracyn contains erithromycin, which is good for gram positive issues. Sometimes, popeye can be caused by gram positive infections.
 
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