Florida's Underwater Archaeology Program is based in the R. A. Gray Building in Tallahassee. The Gray Building houses the Museum of Florida History, the Florida State Archives, the State Library of Florida, and the offices of the Division of Historical Resources, including Bureau of Archaeological Research and its Research and Conservation Laboratory.

In 1990, the Florida Bureau of Archaeological Research initiated the Pensacola Shipwreck Survey to conduct a pilot study of Pensacola Bay shipwrecks and to prepare a regional model for their management and protection. Over the course of two years, forty wrecked or abandoned vessels were studied, ranging in size from a 14-foot wooden punt to a 450-foot steel battleship, and in age from colonial to modern times. The sites were located by consulting historical records, local fishermen and divers, and by sophisticated electronic sensing equipment, including a variety of instruments that were towed along the bottom of the bay to detect man-made deposits.

The Historic Pensacola Preservation Board with its direct support organization Historic Pensacola, Inc., is situated in the city's waterfront historic district. The Board manages three state museums as well as a number of historic buildings and exhibits, and has established a strong local community support network. Given its public mission and central role in historic preservation, the Board, under the direction of John Daniels, was invited to become a partner in the shipwreck project. A conservation laboratory to treat artifacts from the Emanuel Point Ship was established in the basement of this building, the T. T. Wentworth, Jr. Florida State Museum.

To treat over 3,000 waterlogged artifacts and field specimens from the shipwreck, the conservation laboratory employs a conservator, John Bratten and graduate student interns and many volunteers from the local community. Metal, ceramics, wood, and organic materials undergo various treatments to stabilize their condition after over 400 years underwater so that they can be studied and displayed. Guided by x-ray film of the encrusted iron artifact, Field Technician Chuck Hughson uses a small air chisel to mechanically "excavate" through concretions that have built up over the centuries.

The University of West Florida agreed to become an academic partner in the investigations of the Emanuel Point Ship, not only for the shipwreck's research potential for students, but due to the University's record of public-oriented archaeology in the Pensacola community. This partnership also was seen as a way in which UWF could begin to develop a capability in marine archaeology at the graduate level. Together with Dr. Judy Bense, director of the University's Archaeology Institute, a plan was developed to offer students opportunities to enroll in formal courses and fieldwork focused on the Emanuel Point Ship.