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Ouch. Poor little guy. I would:

1) Do 50% weekly water changes.

A 3 gal tank with a filter, even if cycled, should still have at least 50% weekly water changes.

You said the ammonia is "normal." Do you know a more specific number or reading?

Even if there is no measurable ammonia, it's still important to do weekly water changes of about 50% to remove organic wastes, bacteria and other toxins. These won't show up in an ammonia test, but they're still present in the tank.

2) Switch his food to a quality high-protein pellet.

Aqueon and Tetra Tropical Medley contain a lot of filler/grains. These can cause bloating in some bettas. On this forum, two foods are often recommended:
-- New Life Spectrum, and
-- Omega One.
These two brands are well-tolerated by Bettas, and seem to cause fewer digestive issues than other brands.

3) I would add Epsom salt to the tank.

Epsom salt has a fluid reducing and laxative effect (in both people and fish). It's available at supermarkets and pharmacies (but not petstores). Get plain magnesium sulfate. There should be no dyes or perfumes in it. It's inexpensive. A small container should cost about $1 and will last a long time.

I would start with a dosage of 1 teaspoon Epsom salt per gallon. Here is one way to do this:
- Put some tank water in a cup.
- Stir in 0.5 teaspoons Epsom salt per gallon of tank capacity. (Ie: 1.5 teaspoons for your 3 gal tank.)
- Once the salt is completely dissolved, pour the solution into the tank....
- Wait at least 30 minutes, then repeat the above process.
This will bring it to a dosage of 1 teaspoon Epsom salt per gallon.

Keep him in the Epsom salt treated water for now. It can take several days for it to begin working.

4) If the Epsom salt is not effective in several days, try metronidazole.

Metronidazole is effective against anaerobic bacterial infections, as well as many parasites. I would try a combination metronidazole/praziquantel combination, such as API General Cure. This is a relatively mild treatment.

5) Keep us updated.

Continue to provide updates, and post photos so that we can see how he's doing.

3,952 Posts
@InStitches -

Fish are small. It's difficult to know where to pierce the area. All the internal organs are close together, which means that there's a risk of piercing something vital.

The cyst may be fluid-filled, or it could contain gases (not necessarily the same ones that make up air).

If his swimming isn't affected, it's likely filled with fluid. (That much gas would pull him towards the surface. On the other hand, a fluid would have a density closer to the tank water, which would allow him to maintain his buoyancy.)
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