After completing the course of instruction, he was detached from the Naval Academy on 1 June 1885 to await orders for the two years of sea duty that preceded graduation at that time.
Following service in Tennessee and Richmond, he returned to Annapolis in the spring of 1887 for graduation, received his diploma on 15 June 1887, and was commissioned an ensign on 1 July 1887.
During the next three years, Rust served successively in the Bureau of Navigation and the sloops of war Saratoga, Constellation, and Jamestown.
Following four months of ordnance duty at the Washington Navy Yard, he reported to the Naval Proving Ground at Indian Head, Maryland, on 7 April 1892 for similar service.
After a tour of duty ashore at Bath, Maine, as inspector of equipment and ordnance, he returned to sea in Montgomery in July 1902 and served in her until September 1904.
In November 1907, he reported to the Bureau of Equipment in Washington in conjunction with preparations for a hydrographic survey of the southern coast of Cuba between Cape Cruz and Casilda.
Late in October, he returned to Cuba to resume direction of the hydrographic survey and to assume command of Hist.
Rust was called back to active duty on 4 April 1917, two days before the United States entered World War I.
Early in June 1918, he was transferred back to Philadelphia where he served on the staff of the Commandant, 4th Naval District, chairing boards investigating maritime mishaps.