Port Saint Joe, Florida is located on the site of a deep water natural harbor that has served twice as a thriving port over the last 180 years.

The first port development was during the late 1830s and early 1840s. The town of St. Joseph was formed by a group of wealthy promoters so that it could compete with Apalachicola for the export of large cotton crops from Georgia and Alabama as well as other locally produced commodities such as naval stores and lumber. Florida's first railroad was built from Lake Wimico to St. Joseph Bay. Much of the cargo that would normally be shipped to The Port of Apalachicola was now detoured into the lake where it was off loaded and transported by rail to ships docked at St. Joseph.

During this boom period between 1832 and 1842, the sea shore along St. Joseph was defined by long wharves extending almost 4,000 feet into the sea. The Port also had a shipyard with many large warehouses scattered about. During the height of the first Port's existence, it easily competed with well-established ports such as Charleston and New Orleans. The local newspaper during that period, the St. Joseph Times, reported that "up until December 23, 1839, the cotton shipments alone would exceed 50,000 bails". Most of the exports from the Port at St. Joseph were shipped to New England or to overseas ports in Europe.

The Port was the growth engine for Old St. Joseph, and a growth engine it was. In a few short years after establishing the port, the town of St. Joseph soared to a population of 12,000 people and became the largest city in this new territory. The city was so charming and well known that in 1839 it hosted an assembly of statesmen for the purpose of establishing a state constitution.

The fate of St. Joseph and its splendid port however had only a short existence. In the summer of 1841 a ship sailed from Cuba into the Port of Port St. Joseph. Along with its cargo, it carried a passenger infected with a disease transmitted primarily from the bite of the mosquito. It was the dreaded disease, yellow fever, and it quickly spread throughout the town. Within a short month, the town was all but deserted. Those the yellow fever did not kill escaped to faraway places, never to return to this former city of death. The town of St. Joseph never recovered from the loss it sustained during this epidemic of yellow fever. The long docks and the waterfront buildings that dotted the shore line began to deteriorate from lack of maintenance and upkeep. It wasn't long however before they were completely destroyed. As told by historian Dale Cox, "In September 1844, a hurricane struck St. Joseph, destroying much of what remained of the community and driving away some of the last inhabitants".

Except for occasional small supply ships in and out of the port, this natural deep water harbor remained idle and undeveloped until around 1910 when the railroad was again activated. Piers jutting approximately 1,800 feet into the bay were constructed with railroad tracks so that ships could load and unload directly to the railroad cars parked alongside. This design of the piers with tracks laid along the top was an efficient way to handle the incoming and outgoing cargo from the old sailing vessels as well as the new steam vessels that were increasingly taking their place.

The Port again had considerable shipping activity which lasted until, as former postmaster Henry Drake noted, "The Wall Street Crash of 1929 caused a sudden and sharp decline in foreign and domestic shipping". This decline caused financial hardship for The Apalachicola Northern Railroad and as a result, it was sold in 1933 to the Alfred I. DuPont company. Mr. DuPont purchased the railroad line which now extended from Chattahoochee to Port St. Joe, Florida with the intent of using its infrastructure to build a modern paper mill that would utilize the resources from over 200,000 acres of timber land that was purchased along with the existing rail line. Mr. DuPont died in 1935 but, as a fulfillment of his vision, the St. Joe Paper Company was founded in 1936 as part of the Alfred I. du Pont Testamentary Trust. The construction of the paper mill began in 1936 and was completed in 1938. Also completed in February of 1938 were the new St. Joe Paper Company docks. According to former Postmaster Henry Drake, they "were made of the latest type of sheet piling driven into the bay bottom", and "the docks and wharves were capable of loading and unloading, simultaneously, five of the largest ocean-going boats in the Gulf of Mexico trade and still have room for a similar handling of two or more smaller and lighter draft vessels".

In 1941, on a site just south of the paper mill, which is currently "jetty park," the oil docks portion of the port was built along with a large tank farm that extended from the docks to where the current Centennial Bank is now located. Petroleum products were shipped in from the oil fields of Louisiana and Texas in large tankers and barges. The petroleum was then pumped to Chattanooga, Tennessee and intermediate points via an 8 inch pipeline that was constructed during the same time the oil docks were being built. By 1963 the petroleum distribution center had reached its life cycle and was therefore shut down. In the early 70's Hess oil purchased the facility and operated it until the mid to late 80's when it was then shut down permanently.

From 1938 to the early 1970's the Port of Port St. Joe enjoyed a brisk national and international trade. In the 1950's, at the height of the port activity, there were ships coming out of and going in to the Port on a weekly basis. Beginning in the early 1970's however, shipping from the Port began a steady decline and by the mid 1980's most shipping activity had ended. By 1996 the natural deep water harbor and the extended channel that led to the open waters of the Gulf of Mexico experienced its last visit from a cargo ship.

Currently the bulkhead and surrounding land sits idle awaiting a new birth. The former major users of the Port area include the St. Joe Paper Mill and Box Plant, and the Arizona Chemical Company which have been razed so that the land can be reclaimed for further use. Also, left behind is the essential infrastructure used to support their operations. Water, sewer, electricity and gas are in abundant supply. The AN short line railroad that connected the Port to the main rail lines of the United States will soon be repaired and back in service. The State of Florida issued a grant to complete environmental and engineering studies of the shipping channel, a requirement before any dredging can take place. The US Army Corps of Engineers issued the Federal Permit in February 2015 to dredge the shipping channel up to 37 feet, and the Florida Department of Environmental Protection issued the State Permits in December 2014 to dredge the shipping channel up to 37 feet with disposal of dredge materials in two nearby locations.

The Florida Department of Transportation awarded a $1 million grant to the Port St Joe Port Authority to fund final design of the dredge material disposal areas and to prepare specifications and bid documents for their construction in November 2015. The intent is to advance that project to "shovel ready" status so that implementation of the dredging project, when authorized, will not be delayed.

As a result of a recent formation of a strategic development partnership with the St. Joe Company the Port of Port St. Joe and the surrounding land and infrastructure are now positioned to once again become a thriving port.