[4] In 1974, Dr. Dennis O'Connor of the University of Miami and Dr. Rezneat Darnell of the American Institute of Biological Science nominated the area left unprotected by the boundary change for consideration as a national marine sanctuary.

The designation ceremony took place on December 18, 1975,[1][2] aboard a glass-bottom boat over the reef, attended by NOAA Administrator Dr. Robert White, members of the United States Congress, and officials representing the Government of Florida.

[1][2] As Wellwood approached the reef, she created a grounding track 20 metres (66 ft) wide that removed one of the sanctuary's mooring buoys and damaged bottom substrate up to 6 metres (20 ft) deep, knocking over or otherwise damaging 13 coral heads and leaving her bottom paint embedded in exposed coral skeletons.

[11] Salvors finally refloated and removed Wellwood after 12 days on the reef, and NOAA biologists found that few corals survived the grounding.

[13] Both articles were part of an effort to draw the public's attention to the detrimental effect of human activities on the reef systems in the Florida Keys.

[10][13] In June 1987, the United States Department of the Interior released a five-year plan to open Florida's coastal areas to offshore oil and gas development, with lease sales starting in late 1988.

[2] Public concern over the environmental problems and the prospect of offshore drilling prompted the United States Congress in 1988 to both reauthorize the National Marine Sanctuary program and order NOAA to conduct a feasibility study of the possibility of expanding national marine sanctuary sites in the Florida Keys.

[10] Accordingly, in 1988 NOAA made Alligator Reef, Sombrero Key, and American Shoal official study areas for potential inclusion in national marine sanctuaries.

[14] In 1989, public hearings took place on offshore drilling plans in the Florida Keys, further heightening concerns over the future environmental health of the area.

[2][10][14] Three major ship groundings in the Florida Keys over an 18-day period between October 25 and November 11, 1989, destroyed hundreds of acres (hectares) of coral reef, giving greater impetus to efforts to increase the protection of the area.