William Jones Rhees was born on March 13, 1830, in Philadelphia, Pennsylvania.

He was a famous clerk and secretary of the Smithsonian Institution, writer, and editor. He graduated from Philadelphia's Central High School in 1847 and took a position as clerk and draughtsman for the Holland Land Company in Meadville, Penn. In 1850, he moved to Washington, D.C., and was appointed a clerk in the Census Office in the Department of the Interior. In 1855, he became a chief clerk at the Smithsonian Institution. In 1870, he left briefly to pursue the stationary business in Springfield but returned as chief clerk and secretary. He became the first keeper of the Archives in 1891. Rhees was a prolific writer and editor of Smithsonian history. He wrote An Account of the Smithsonian Institution in 1857, which briefly described the history and organization of the Institution and served as a guide to the National Museum. He also produced several further editions of the Account and Visitor's Guide to the Smithsonian Institution (1880-87, 1889, and 1891-92). He compiled and edited The Smithsonian Institution: Documents Relative to Its Origin and History (1879). He helped found and served as president of the Young Men's Christian Association of Washington and was active in its philanthropic work during the Civil War. He was a member and officer of the District chapter of the Sons of the American Revolution, and he compiled the Register of the District of Columbia Society of the Sons of the American Revolution (1896) and its Yearbook (1897). He was also a member of the Anthropological Society, the District of Columbia Historical Society, the National Geographic Society, and the Pennsylvania Historical Society. Rhees served as a correspondent on special topics for many national and local newspapers.

In 1856, he married Laura Oliver Clarke (1835–1864), and in 1866, he married Romenia Fontinette Ellis (1846–1923). He died on March 18, 1907, in Washington, D.C.