In 1910, leaders in Toledo, Oregon, obtained voters' permission to form a port district, as allowed by a state law passed in 1909. Ports could tax, borrow, buy, lease, and operate property in order to promote business and obtain public access to waterways. The governor appointed the first five commissioners; later candidates were elected to staggered four-year terms.

The first commission issued $50,000 in bonds, backed by a tax on property owners, and purchased property along Depot Slough on the south edge of town. They built a wharf and dredged from Depot Slough a mile down the Yaquina River, twelve miles from deep water at Newport. In 1914, the port secured federal dredging of Depot Slough and the Yaquina River shoal.

In 1918, the port bought land and leased it to the U.S. Spruce Products Division for a huge mill to cut airplane frames for World War I. The war ended before production could begin, however, and the C.D. Johnson interests bought the equipment and site. By 1923, rail lines from Siletz to Yachats, running through former Indian tribal lands, were feeding the mill with logs. The Johnson lumber mill was sold to Georgia Pacific in 1951, which reopened in 1957 as a pulp mill that was still operating in 2011. The Toledo and Newport commissions cooperated to jointly finance the dredging and ocean jetties at the entrance to the Yaquina River to attract shipping.

Prior to World War I, about 500 people lived in Toledo, with about 5,500 in Lincoln County. Almost everyone in and around Toledo was dependent in some way on logging and the mills. From the 1920s to the present, port activity was overshadowed by the operations of Pacific Spruce, Georgia Pacific, and other mills.

To aid local mills and attract more business, the port campaigned with mills and government agencies to secure dredging legislation. About every ten years, the Army Corps of Engineers deepened Depot Slough and a few shoals upriver, but only to ten feet, deep enough for barges but not for ships. Some logs, lumber, and shingles passed over the Port of Toledo dock, but most went by barge from private mills.

Mills closed periodically during the Depression but boomed during World War II, as C.D. Johnson began building tugboats for the U.S. Army. As the slough silted up, however, the port lost tax revenues and traffic from its wharf declined. The largest amount of waterborne commerce—400,000 short tons in 1930, 715,000 in 1960—ran on the river and bay from the 1920s through the 1960s, before the forest industry declined and Georgia Pacific pulp went by land. Among the port lessees during this period were the Farmers Creamery Cooperative, Andersen Boat Works, and Hoffman Towing.

In the 1960s, water-quality regulations and planning requirements influenced dredging and property development. The port commission relied less on local levies and more on grants and loans from agencies such as the Oregon Business Development Department and the Confederated Tribes of Siletz Indians.

From the 1970s onward, the port commission shifted its intent from shipping to light industrial and recreational sites. The port augmented and beautified its property along Depot Slough, acquired warehouse and business space, built two boat-launching parks downriver, hosted an annual wooden boat show, and began a youth boatbuilding and sailing program. The port also purchased a defunct, private boatyard to provide fishermen a place to haul their boats out and to boost the local economy.

By 1998, the port had over forty moorage and lease agreements, including those with Yaquina Boat Equipment, American Grounding Systems, Wiggins Towing, and Island Wild Seafoods. Annual port budgets rose to a million dollars in 2006. While the port never paid for itself, it provided public access to and promoted business on the waterfront.