Born in Connecticut, Cowles entered the U.S. Naval Academy at the age of sixteen, graduating in 1873. As captain of the battleship USS Kentucky, he sailed around the world with the Great White Fleet in 1908–1909. He commanded the U.S. Pacific Fleet from 1913 to 1914 and the U.S. Asiatic Fleet from 1914 to 1915.

In March 1915, Cowles became one of the first full admirals in the history of the U.S. Navy when the three commanders in chief of the Atlantic, Pacific, and Asiatic Fleets were all advanced to the temporary rank of full admiral while so serving. Upon relinquishing command of the Asiatic Fleet in June 1915, Cowles reverted to his permanent rank of rear admiral.

Cowles retired in August 1915. He died in Redlands, California, on November 27, 1917.

• Midshipman – May 1873
• Ensign – July 1874
• Master – August 1879
• Lieutenant, junior grade – March 1883
• Lieutenant – December 1885
• Lieutenant commander – unknown
• Commander – unknown
• Captain – unknown
• Rear admiral – 1911
• Admiral – March 10, 1915

• Page, Walter Hines; Page, Arthur Wilson (August 1915), "The War Chiefs of the Navy", The World's Work: A History of Our Time, 30, Doubleday, Page & Company
• Hamersly, Lewis R. (1894), The Records of Living Officers of the U.S. Navy and Marine Corps, fifth edition, Philadelphia: L.R. Hamersly & Co.
• Heaton, Dean R. (1995), Four Stars: The Super Stars of United States Military History, Baltimore: Gateway Press
• The Captains of the Great White Fleet