William Sheffield Cowles (August 1, 1846 – May 1, 1923) was a rear admiral in the United States Navy.

In July 1863 he was appointed an acting midshipman at the United States Naval Academy and graduated in June 1867.

Cowles commanded the gunboat, Topeka during the Spanish–American War, and served as naval aide to President McKinley.

He was in command of the battleship Missouri when it collided with the Illinois, and when thirty-three men were killed in an explosion (he was cleared of responsibility in both cases).

On December 2, 1908, Cowles submitted a report, prepared by Lieutenant George C. Sweet, recommending the purchase of aircraft suitable for operating from naval ships on scouting and observation mission to the Secretary of the Navy.