The Department of the Navy is headed by the Secretary of the Navy, also known as the SECNAV in naval jargon, who has the authority to conduct all of the affairs of the Department: subject to lawful authority, the Secretary of Defense, and the President.
The highest ranking military officers in the Department of the Navy are the Chief of Naval Operations and the Commandant of the Marine Corps, who are the principal military advisors to the Secretary of the Navy.