Dr. Spence's past work has been funded by such institutions as the Savannah Ships of the Sea Museum, the College of Charleston, the South Carolina Committee for the Humanities and the National Endowment for the Humanities. In 1991 and 1992, Spence served as Chief of Underwater Archeology for San Andres y Providencia, a 40,000 square-mile Colombian owned archipelago in the western Caribbean. He has worked on the wrecks of Spanish galleons, pirate ships, Great Lakes freighters, modern luxury liners (cruise ships), Civil War blockade runners and submarines.
Spence first reported the discovery of the Civil War submarine Hunley in 1970. Spence mapped and reported its location to numerous government agencies. The July 2007 cover story in U.S. News & World Report noted that the Hunley "disappeared without a trace" until 1970 when it was found by "underwater archaeologist E. Lee Spence." That report made no mention of novelist Clive Cussler, whose organization later (August of 2008) dropped a lawsuit in federal district court against Spence in which it had claimed that they and not Spence had discovered the wreck in 1995. Both sides still claim that they and not the other discovered the wreck.
On September 13, 1976, the National Park Service submitted Sea Research Society's (Spence's) location for H.L. Hunley for inclusion on the National Register of Historic Places. Spence's location for Hunley became a matter of public record when H.L. Hunley's placement on that list was officially approved on December 29, 1978.
Spence's book Treasures of the Confederate Coast, which had a chapter on his discovery of Hunley and included a map complete with an "X" showing the wreck's location was published in January of 1995.
In 1995 the discovery was independently verified by a combined South Carolina Institute of Anthropology and Archaeology (SCIAA) and National Underwater and Marine Agency (NUMA) expedition directed by SCIAA underwater archaeologist Dr. Mark M. Newell and funded in part by novelist Clive Cussler. Later the same year, at the official request of Senator Glenn F. McConnell (chairman), of the State of South Carolina Hunley Commission, Spence donated all of his rights to the wreck to the State.
The Hunley discovery was described by Dr. William Dudley, Director of Naval History at the Naval Historical Center as probably the most important (underwater archaeological) find of the (20th) century." The tiny sub and its contents have been valued at over $40,000,000 making the discovery and donation one of the most significant and valuable contributions ever made to the State of South Carolina.
In addition to the Hunley, Spence has discovered several historically significant shipwrecks, including the SS Georgiana (said to have been the most powerful cruiser built by the Confederate States of America).
South Carolina's law protecting both the State's and the salvors' interests in shipwrecks was passed following Spence's discovery of the Georgiana and his company Shipwrecks Inc. was granted South Carolina State Salvage License #1.
Spence states he has salvaged over $50,000,000 in valuable artifacts and has been responsible, through his archival research, for the location of the wrecks of the side-paddle-wheel steamers Republic and Central America from which over one billion dollars in treasure has been recovered.
On April 4, 1989, Spence announced his discovery that Margaret Mitchell, who had claimed her Pulitzer Prize winning novel Gone With The Wind was pure fiction, had actually taken much of her compelling story of love, greed and war from real life and that Mitchell had actually based Rhett Butler on the life of George Alfred Trenholm, a tall, handsome, shipping magnate from Charleston, South Carolina, who had made millions of dollars from blockade running and was accused of making off with much of the Confederate treasury and had been thrown in prison after the Civil War. Spence's literary discovery that had its roots in his prior discoveries of some of Trenholm's wrecked blockade runners made international news.
The Encyclopedia Of Civil War Shipwrecks by W. Craig Gaines additionally credits Spence with the discoveries of the following Civil War wrecks: the Constance (lost 1864, found 1967); Housantonic (lost 1864, found 1970); Keokuk (lost 1863, found 1971); Minho (lost 1862, found 1965); Presto (lost 1864, found 1967); Ruby (lost 1863, found 1966); Stonewall Jackson (lost 1863, found 1965). Spence own books, as well as numerous third party books, newspaper and magazine accounts, and archaeological reports describe his discoveries of the blockade runners Mary Bowers and Norseman and dozens of other ships of all types and nations in waters all over the world spanning a time period of over two thousand years.