After receiving his commission, Salzer was assigned to the Office of the Chief of Naval Operations until 1942, when he joined the . In March 1943 he assumed command of the coastal minesweeper , and in July 1943 that of the auxiliary motor minesweeper "YMS-347". He then commanded the tank landing ship "LST-624" from June 1944 to December 1945, participating in the Lingayen Gulf landings, the Manila Bay-Bicol operations and the occupation of Okinawa.