Without pictures, I don't think anyone can tell for sure but it is most likely an ear infection/abscess. It's relatively common in aquatic turtles to get it (sometimes due to poor husbandry) and can happen despite our best efforts. Just like humans, they get sick and infected and must be treated.
I'm dealing with the exact same problem with my baby painted turtle's left cheek right this moment. I took him to the vet and the treatment is going to cost $110 (anesthesia, extraction, and medication). They're going to have to cut it semicircularly and scrape out the pus and then let it heal in time. I was actually thinking about doing it myself since I have sterile equipment and medication at my disposal and I have taken care of turtles for over a decade. However, I think the wiser choice was to let professionals deal with something so tiny. Many risks can happen if done incorrectly--more infection, cutting into tendons and bone of the head, excessive bleeding--you get the picture. And I woulnd' tknow the correct dosage of anesthesia (Ketamine & isoflurane) to apply effectively. So it's up to you really if you want to shell out $$$ to get it treated. I know some experienced herpers do it themselves; some get lucky because it ruptures and falls off in time but there is a risk of the infection damaging the underlying bone according to my vet.
Let us know your decision. If you need a qualified reptile vet, go to www.austinsturtlepage.com and click on Vet Listings by state to find one. Bills will be heavy, of course.
Johnny