Arriving in New England at the beginning of the war, Bush enlisted at Portsmouth, New Hampshire, for a three-year term as an "ordinary seaman" on September 27, 1864. During his service, he worked on and later the captured Confederate vessel , which chased blockade runners off West Florida as part of the squadrons responsible for maintaining the blockade of the ports of the Confederacy. He developed chronic laryngitis and spinal injuries due to his service in the Union Navy and was discharged in September 1865 at the Brooklyn Naval Hospital. When the war ended, the impoverished Bush had no way of returning to Hawaii. For the next decade, he lived in New Bedford, San Francisco, and Tahiti, finally returning to Hawaii in 1877. In 1905, after Hawaii became a US territory, Bush was granted a pension for his service in the Civil War, with back pensions dating from May 8, 1897.