The Depot had its origin in 1940 when the Navy bought 500 acres (2.0 km2) of wetlands from the city of Oakland for $1.00.

[1] The 1995 Base Realignment and Closure Commission recommended that the Center be closed.

[2] It was closed in 1998, and in 1999, the Navy transferred the entire 531-acre (2.15 km2) property to the Port of Oakland.

The new owner plans to develop it for intermodal freight transport involving a marine terminal, railroad, and truck cargo activities.

A portion of the supply depot was developed into Middle Harbor Shoreline Park in 2003.