It is a stop on Amtrak's Empire Builder train and is the main hub for Link Transit, the local bus system serving Wenatchee and surrounding areas.

The three-story station building is located in the northeast corner of the block and includes the Link Transit guest services center, a passenger waiting room, offices, public restrooms, and a cafe.

[11] The modern settlement of Wenatchee began in 1890 with real estate developers planning a town along the proposed route of the Seattle, Lake Shore and Eastern Railway, which was never completed.

The Empire Builder was moved to the former Northern Pacific Railway route between Seattle and Spokane via Stampede Pass, leaving Wenatchee without passenger rail service.

[22][23] On June 13, 1973, Amtrak restored passenger rail service to Wenatchee by moving the tri-weekly North Coast Hiawatha to the Stevens Pass route.

[24] During the 1974 World's Fair, hosted in Spokane, Amtrak ran a daytime train along the North Coast Hiawatha route that stopped in Wenatchee and Ephrata.

[27] Amtrak restored rail service to Wenatchee a second time on October 25, 1981, by rerouting the Empire Builder over Stevens Pass and installed a plastic shelter at Kittitas Street to serve as a temporary station.

[28][29] The city government began lobbying Amtrak and Burlington Northern for the construction of a permanent passenger rail station adjacent to the Wenatchee Convention Center on First Street.

[35] After outcry over the project's budget and a plan to condemn an adjacent parking lot,[36] Link Transit began considering a new site for the facility that would be eligible for state and federal funding.

[39] Several options for the Kittitas Street site were considered by Link Transit, including a separate waiting area for Amtrak passengers and the orientation of the bus bays.

[45] Construction costs for the project were lower than expected, allowing for Link Transit to re-add several decorative features that had been deferred in the planning process, including the street clock.

[52] Columbia Station is the main hub for Link Transit, a regional bus system that serves Wenatchee and other communities in Chelan and Douglas counties.

[56] Private coach operator Northwestern Trailways has an office at the station and runs daily buses from Wenatchee to Omak, Ellensburg, Everett, Seattle, Tacoma, and Spokane.