Although there are no Interstate highways in Wakulla County, several major routes do pass through the area, including U.S. Route 98 and U.S. Route 319. Other important roads in the county include State Road 267, State Road 363 and County Road 375.
The Wakulla County Airport (2J0), located south of Panacea, is a small public-use airport with a single 2600-foot, north-south turf runway.
St. Marks is a small commercial seaport, currently used primarily by commercial fishermen and recreational boaters. Panacea and Ochlockonee Bay also support small fishing fleets.