His death in the sinking of the Brother Jonathan in July 1865 was one reason that the mint was never completed.
In 1864, the U.S. Congress agreed to establish a branch of the United States Mint in The Dalles to manage the flow of gold and help fund the ongoing American Civil War.
In 1865, having established his reputation as an Indian agent, Logan was appointed the superintendent of the U.S. branch mint at The Dalles.
He and his family were in San Francisco in 1865, and boarded the Brother Jonathan on July 28 to return to Oregon.
Both William and his wife perished when the ship ran aground and sank on July 30.