Through most of the 19th century and the first half of the 20th, Deer Island was owned and occupied by the Baker Family, descendents of Josephus Aiken, who acquired ownership by a patent signed by President James K. Polk. In 1951, Robert D. Sanders, an industrialist and philanthropist from Jackson, Mississippi, purchased all but the western extremity of the island. The last of the Aiken and Baker descendants had moved to the mainland by that time, but the family retained ownership of a portion of the island.
In subsequent years, the island remained unoccupied. The abandoned structures on the island were destroyed by times and the elements, and the island reverted to its natural state. With the advent of casino gaming in 1992, pressure mounted for commercial development of Deer Island.
In 2002-03, Secretary of State Eric Clark organized a coalition to arrange for purchase of Deer Island by the State of Mississippi, so that the island could be preserved for the recreational use and enjoyment of the public. The heirs of Robert D. Sanders shared this vision of the future of Deer Island. They agreed to sell their interests so that the project could proceed.
The U.S. Congress provided substantial funds on a matching basis for distribution by the National Oceanic and Atmospheric Administration through the Coastal and Estuarine Land Conservation program. The Mississippi Legislature provided state funding through the issuance of bonds. Additional funding came from the Secretary of State's office and the Commission on Marine Resources. The entire project was facilitated by the Trust for Public Land. Deer Island is now a part of Mississippi's Coastal Preserve System.