The turtle should be soaked in a dilute povidone-iodine bath. The areas of infection can then be gently scraped away using a blunt edge such as a table knife. The scraped areas are then swabbed with povidone-iodine solution or ointment. Fungal and bacterial shell rot typically occurs in aquatic turtles. Pits of varying size and depths have also been found in terrestrial chelonians, typically the result of the animal being preyed upon by invertebrates while in hibernation.
Treatment is the same as for aquatic turtles.
Deep erosions may be sealed with fiberglass cloth and epoxy resin after the underlying tissues have been cleaned. The conditions that caused the shell rot to begin with must be addressed concurrent with treatment. Typically, this means cleaning and disinfecting the tank and keeping the water clean by use of a regularly serviced filtration system and frequent water changes. During the recovery process, the turtle should be kept dry and out of the water as much as possible, allowed in daily to feed, drink and defecate only. If the rot has penetrated into the shell, or you are not sure if it has, you should take the turtle or tortoise to an experienced reptile vet.