The Port of Ilwaco is located on the inland side of the Long Beach Peninsula at the mouth of the Columbia River in western Washington. The Port of Ilwaco is about 11 nautical miles (21 kilometers or 13 miles northwest) across the river from the Port of Astoria, Oregon. The Port of Ilwaco is some 86 nautical miles downriver (125 kilometers or 77 miles northwest) of the Port of Portland, Oregon. The 2010 US Census reported a population of 936 in the Port of Ilwaco.

For as long as 2500 years, the Chinook people populated the Long Beach Peninsula and the future Port of Ilwaco. Their legends say that the ancient Taanewatiks settled there because the strong Columbia River currents kept them from entering the river. From the mouth of the Columbia, the Chinook moved inland from the Port of Ilwaco area, settling the lands around the long river.

Chinook society contained castes, with the top levels being shamans, warriors, and traders. Some Chinook owned slaves that stole for their masters. Chinook of high social status bound their children's heads to flatten them, and Europeans arriving in the future Port of Ilwaco called them the "Flathead Indians." The peaceful Chinook were non-nomadic fur traders, elk hunters, and fishermen that lived in longhouses occupied by as many as 50 people.

The Chinook were the people that met Lewis & Clark in 1805 when they explored the Columbia and Long Beach peninsula, future home of the Port of Ilwaco. When white settlers arrived, the Chinook population was decimated by disease. At the turn of the 19th Century, the Chinook Nation contained many tribes and a population of about 16 thousand. Blessed with abundant natural resources, the Chinook did not have to work hard for their food. Rather than warfare, they preferred water challenge rituals.

Today, the Chinook seek federal recognition. Many of their people live on reservations in Washington and Oregon. With over 2000 registered members, hundreds of Chinook have membership applications pending with the tribe.

The Port of Ilwaco was settled first in 1851 by Henry Feister. The town was incorporated in 1890.

For more than 30 years, the Ilwaco Railway and Navigation Company operated in the Port of Ilwaco. The railroad ran up what is First Street today in the Port of Ilwaco. A rail siding was constructed for the Ilwaco Mill and Lumber Company. The old freight depot is part of today's Ilwaco Heritage Museum. The train extended to the dock in the Port of Ilwaco. Floating logs awaited loading behind log booms adjacent to the Port of Ilwaco dock.

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