John B. Mooney Jr. (26 March 1931 – 30 May 2014) was an American naval officer, oceanographic engineer, and deep submergence specialist who advanced undersea technology and exploration. He served as officer in charge of the bathyscaphe Trieste II, piloting dives to wreck sites including the nuclear submarines Thresher and Scorpion, and later held leadership roles as oceanographer of the Navy and chief of the Office of Naval Research. Mooney also contributed to civilian ocean science, serving as president of the Harbor Branch Oceanographic Institution and as a member of the National Academy of Engineering.