Upon his resignation from the U.S. Navy, the Virginia governor appointed Maury commander of the Virginia Navy. When this was consolidated into the Confederate Navy, Maury was made a commander in the Confederate States Navy and appointed as chief of the Naval Bureau of Coast, Harbor, and River Defense. In this role, Maury helped develop the first electrically controlled naval mine, which caused havoc for Union shipping. He had experience with the transatlantic cable and electricity flowing through wires underwater when working with Cyrus West Field and Samuel Finley Breese Morse. The naval mines, called torpedoes in that time, were similar to present-day contact mines and were said by the Secretary of the Navy in 1865 "to have cost the Union more vessels than all other causes combined.