The Saint Joseph Bay makes Port St. Joe a well-protected harbor. Today, Port St. Joe consists of two port properties covering a total of 132 acres (53.5 hectares). The Port St. Joe Port Authority is developing Port St. Joe in phases. In Phase I, important improvements were made including the addition of 267 meters (876 feet) of bulkhead, an access road, and the purchase of rail service. Environmental permitting and dredging for deep-water berths in Port St. Joe is nearing completion. The next phase includes financing and securing partners for the construction and operation of a deep-water component for Port St. Joe.

The Florida Coast Paper Company LLC owns and operates a wharf for receiving caustic soda and fuel oil for their plant and for shipping paper products. This Port St. Joe wharf is served by a 213.4-meter (700-foot) surface track that links the wharf to the paper mean and a storage area at the rear. The rail track also connects with the AN Railroad. Port St. Joe's Florida Coast Paper Company Wharf is linked by an 8-inch pipeline to a 47-thousand gallon caustic soda storage tank and by a 12-inch pipeline to three steel fuel oil storage tanks with total capacity for 115.6 thousand barrels. The Company stores paper products in a 119-by-33-meter (390-by-110-foot) transit shed. Located about 1.4 kilometers (.9 miles) east of the Gulf County Canal, the wharf has berthing space of 457.2 meters (1500 feet) with alongside depth of 8.8 meters (29 feet).

Material Transfer, Inc. owns and operates the Port St. Joe Dock to receive coal by barge. The Port St. Joe Dock is served by two loop rail tracks with total capacity for 100 rail cars. The tracks link the dock to open storage at the rear with capacity for 100 thousand tons of coal, and they connect with the AN Railroad. Located on the east bank of the Gulf County Canal, the Port St. Joe Dock has berthing space of 518.2 meters (1700 feet) with alongside depth of 3.7 meters (12 feet). There is also about 457.2 meters (1500 feet) of berthing space for idle barges on the opposite side of the canal.

The Port St. Joe Marina is a popular stopping point for boaters using the Gulf Intracoastal Waterway. Amenities available to visiting boaters include transient slips, a 137.2-meter (450-foot) lay-a-long transient dock, wet slips, and dry boat storage. The Port St. Joe Marina has high-volume fuel pumps for gas and diesel fuel. Also available are a gift shop, a restaurant, toilet and shower facilities, a laundry, and boat rentals as well as charters for fishing and events.

The six-acre Port St. Joe Marina basin has 133 wet slips (22 covered), 72 of which have electric service, and 77 dry storage spaces. Average depth in the Port St. Joe Marina is two meters (6.5 feet). The Port St. Joe Marina can accommodate yachts to 36.6 meters (120 feet) long with 2.1-meter (7-foot) draft.

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