This 100-acre migratory bird refuge began as a one-acre oyster shoal. The U.S. Army Corps of Engineers (COE), while engaged in river and harbor improvements, used the shoal as a spoil site. Accumulated spoil created Oysterbed Island (the nucleus of the present refuge). Title to Oysterbed Island was conveyed to the United States by the state of Georgia on December 30, 1820. Since that time, the COE has continued to use the area as a spoil site. Accumulated spoil eventually joined Oysterbed Island and Jones Island to form the north bank of the Savannah River.
Tybee NWR was established by Executive Order No. 7882 on May 9, 1938 "in order to effectuate further the purposes of the Migratory Bird Conservation Act". In the enabling legislation, the United States Coast Guard (USCG) retained control over a one-acre site known as the Oysterbed Lighthouse Reservation and the COE retained the authority to deposit soil on the refuge. The legislation does stipulate "that any accretions thereto resulting directly or indirectly from river and harbor improvement work shall when formed become part of the refuge". The USCG transferred the Day Beacon Tower and surrounding area (formerly the Oysterbed Lighthouse Reservation) to the U.S. Fish and Wildlife Service on February 17, 1960.