Additional lands from Ware County, Georgia, were added to Charlton's borders by an 1855 act of the General Assembly.

A large portion of the county lies within the Okefenokee Swamp and its federally protected areas.

The entire central and southern portion of Charlton County is located in the St. Marys sub-basin of the St. Marys-Satilla basin.

The county's northeastern portion, north of Homeland, is located in the Satilla River sub-basin of the St. Marys-Satilla basin.

[8] The country's southern region is level with the northernmost part of the central and eastern Panhandle of the Florida peninsula.