This used to happen to Tank all the time when he was younger, as the result of the stupid basking lamp. I used the "Turtle Eye Drops" sold at both PetCo and PetSmart with great success. For most of this past year, he would get 2 drops in each eye once a week. I'm now using an ExoTerra ReptiGlo 5.0 lamp with great success and no photokeratokonjuntivitis (I butchered the spelling, sorry.)
I also quit using chemicals almost entirely in his water. No more of that stuff that breaks the leftover food down and no random water-balancers, algae solution, et cetera. Very occasionally I add some ReptiSafe, but this is usually after a 50-70% water change. Tap water is totally fine for RES, so long as there isn't anything terribly funky in the water in your location.
However, I really feel like 80% of the time it's the basking lamps that mess their eyes up, and not so much the water quality because RES can get along fine in all kinds of water as long as there isn't a proliferation of random chemicals.
I don't think it's anything serious to worry about at all, not unless they start exhibiting serious signs of RI. But swollen eyes is a really common problem, and it happened to my turtle ALL THE TIME when he was young, so don't worry yourself by assuming they have pneumonia.

Get the Turtle Eye Drops, do those once a week, and move the lamp 12 inches away from the basking area. Also, go ahead and do a water change and see if their eyes don't improve.