This is good advice above. However, since popeye is a symptom of something else and not an actual disease (much like dropsy) it's important to pinpoint the source of it and adjust.
It seems to me that your problem is not frequent enough water changes.
Most people will tell you that you can't ever fully cycle a tank under 5g, despite your filter, and you will always need these changes.. you can try, but careful daily monitoring and reliable test kits should be used. This is for tanks 2.5G+. Anything less and there’s no point in even trying. You need to be testing daily with a reliable drops kit for ammonia and nitrite and doing an extra 50% change any time you see either. In addition to this a weekly 50% with siphon or new fresh turkey baster that has never seen chems is needed to remove poop and other debris from the gravel. It is not enough to just scoop water off the top ever. I actually suggest a turkey baster or very small siphon because your tank is so small an average siphon will remove water too quickly.
First you will see ammonia, then nitrite. Eventually, hopefully, you will see ammonia fall and stay at 0 even after a week of no water changes, and finally nitrite. At this point you will be left with only nitrates after a full week of no changes and these can be kept <20ppm by twice weekly 50% change with baster/siphon. However, cycling will take up to two months to complete and many if not most people will tell you that you can't cycle a tank of this size and you will always need twice weekly 50% and 100% water changes or you will always see ammonia continuing to build and the cycle will never finish..
Also there's a lot of reasons that the cycle could seem to finish and then eventually break back down.. one problem with tanks and filters that fit it is that they generally only have one type of media. However, replacing all media at once wipes out your biofilter and requires recycling every time. This is a major flaw in small filters
Right now he's not fit to use to cycle. You should increase water changes to 50% every other day and 100% by week's end. Do changes like this to avoid shock.
The 50% changes the betta can be kept in the bowl and use a turkey baster to remove half the water and as much of the debris as possible. For the 100% you need to remove him - scoop him out with a plastic solo type cup and set aside while you thoroughly rinse the bowl and gravel to remove the debris. Then he should be acclimated to the new water by floating for an hour while you slowly add a couple tablespoons of new water to the cup every 10 minutes. When you release him, try to let as little of the old cup water back into the tank as possible. All water changes should use same temp water, matched to running tap using the in tank thermometer and the water needs to be premixed with conditioner before adding it to the betta tank. If you don't already have anything, you can use gallon water jugs from the grocery store - rinsed thoroughly in hot water but no chems.
The ES you only add back along with a water change, and you only add as much as water you change. It also needs to be pure 100% magnesium sulfate with no additives, dyes, perfumes, etc of any kind. I get mine from CVS Pharmacy. It also needs to be predissolved outside the tank is some tank water in separate cup/container. It should START with 1 tsp per gallon, and add slowly over an hour. Wait 12 hours before adding the second tsp. If you just dump that much in at once you risk major ph shock.
Last edited by callistra; 03-13-2013 at 10:12 PM.