Carpenter obtained permission from NASA to take a leave of absence to join the U.S. Navy SEALAB project as an aquanaut. During training he suffered injuries that grounded him, making him unavailable for further spaceflights. In 1965, he spent 28 days living on the ocean floor off the coast of California as part of SEALAB II. He returned to NASA as Executive Assistant to the Director of the Manned Spacecraft Center, then joined the Navy's Deep Submergence Systems Project in 1967 as Director of Aquanaut Operations for SEALAB III. He retired from NASA in 1967, and from the Navy in 1969.