The Port of Skagit is located in La Conner, Washington, in the Puget Sound area. The Port of Skagit is about ten nautical miles (16 kilometers or 10 miles), through the Swinomish Channel, southeast of the Port of Anacortes. Via Skagit Bay, the Port of Skagit is about 56 nautical miles (89 kilometers or 55 miles) north-northwest of the Port of Seattle. In 2011, there were almost 900 people living in the Port of Skagit's home city of La Conner.

In pre-Columbian times, the Upper Skagit lived in what would become the State of Washington. Archaeological evidence suggests that humans had lived in the area as long as 8500 years ago. A Salish-speaking people, the Upper Skagit lived along the Skagit, Baker, and Sauk Rivers. When Europeans began to arrive, they lived along the Skagit River from Diablo to the mouth of the River. The Upper Skagit lived in cedar longhouses and subsisted mainly on salmon. They practiced basket weaving to store the fish they caught.

In the 17th Century, explorers from Spain and England entered the area of the Puget Sound tribes, but it would be many years before white settlers followed. Settlement brought conflict, and the territorial governor and Indian agent, Isaac Stevens, negotiated the Point Elliott Treaty in 1855 that basically forced 80 tribal leaders to cede their lands. Because the territorial government did not recognize the Upper Skagit as a distinct group, they were not assigned a reservation.

Without reserved land, many Upper Skagit moved to other states. It was the 1970s before the tribe gained formal federal recognition and acquired a small reservation of federal trust land. In 1995, they opened the Skagit Valley Casino Resort, giving the Upper Skagit an alternative to fishing and logging. They also bought an interest in the Semiahoo Resort in Blaine, Washington. Their reservation is located on three different land parcels in western Skagit County. In 2000, about 238 people lived on the reservation.

Skagit City was created when Barker's Trading Post opened on the river in 1869. The Port of Skagit soon became an important center for river transportation. In the 1880s, the Port of Skagit thrived until Mount Vernon, Washington, began to grow upstream.

During its heyday, the Port of Skagit provided sheltered harbor for sternwheelers moving between Seattle and small towns in the southern Puget Sound. The Fanny Lake was the ship to navigate the route between Seattle, the Port of Skagit, and the growing La Conner.

Skagit City was a river town with a narrow settled area that stretched along the river. Many boats, including a ferry, docked at the Port of Skagit harbor. At its peak, Skagit City held many shops, churches, hotels, and houses as well as a school and a saloon.

In the 1870s, two logjams that had clogged the river and blocked upstream traffic were removed. Mount Vernon began to grow rapidly, and the Port of Skagit began to lose businesses and residents. By 1906, only one building stood at the site of Skagit City. By World War II, there was nothing left of the town. "Skagit City" became a place name, but the Port of Skagit survived.

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