Hi Paul,
Since you say he's 5 years old, is he captive bred? If so he probably has some shell fungus. You can apply some triple antibiotic to slow the infection. Sometimes this happens due to sitting in soiled substrate.
If the turtle is originally wild caught, it is quite common for both Gulf Coasts and Floridas to have some level of shell rot from sitting in highly acidic water which can lead to some shell degradation and be more susceptible to similar infections.
Treatment is pretty much the same either way. You can see some improvements but if the infection is deep, it is not reversible.
If its really bad, I would have a vet check it. He/she can perform some pathology to determine the source and treatment options.
Paul