The history of the coral reef exhibit began in 1980 at the Smithsonian Institution's National Museum of Natural History in Washington, DC. After many years of research, Smithsonian scientists were the first to put a living model of an Atlantic coral reef ecosystem on display for the public. The exhibit remained one of the museum's biggest attractions until 1998, when the decision was made to replace it with new displays. To take advantage of this unique opportunity, the Smithsonian Marine Station in Fort Pierce and St. Lucie County formed a partnership and began to make plans to move the exhibit to Fort Pierce. The plan was to expand the exhibit to include the major habitats of the Indian River Lagoon and adjacent coastal waters.

The vision became reality in November 2000, when the St. Lucie County Board of Commissioners gave their final approval for construction of the St. Lucie County Marine Center to house the Smithsonian Marine Ecosystems Exhibit. St Lucie County with help from the City of Fort Pierce, constructed the 5,141 square foot facility in a county park across from the campus of the Smithsonian Marine Station at Fort Pierce. Additional support came from the St. Lucie County School District, the Fort Pierce Utilities Authority, the Indian River Community College, the South Florida Water Management District, and the St. Johns River Water Management District.

The Marine Center opened on August 29, 2001. The facility  features six aquarium displays of habitats typical of the Indian River Lagoon and surrounding coastal waters.  The Smithsonian Marine Station sponsors the exhibit and is responsible for the development and maintenance of all displays and public outreach.