The papers of Samuel Phillips Lee, naval officer and farmer, consist of miscellaneous writings and notes, diaries, memoranda books, and account books (1858-1896), logs and journals (1847-1866), correspondence, documents, naval records (1861-1872), maps, photographs, memorabilia, artifacts, miscellaneous material, printed matter, and papers of others. Although a professional naval officer (1825-1873), Lee spent his retirement years (1873-1897) at Silver Spring Farm, the management of which had been transferred to him by his father-in-law, Francis Preston Blair. The collection reflects these dual careers as well as Lee's business interests in real estate, especially holdings in St. Louis, Missouri, Maryland, and Washington, D.C. An avid record keeper and commentator, his logs, journals, notebooks, and correspondence contain memoranda of explanation and insightful personal notations.

Of special interest is the correspondence between Lee and his wife, Elizabeth Blair Lee, during the long periods when he was at sea and she remained at home in Washington, D.C., observing and reflecting on the political and social scenes, especially during the Civil War years (1861-1864). The Civil War correspondence of Elizabeth Blair Lee, dating from December 5, 1861 to March 4, 1865, has been published in Wartime Washington: The Civil War Letters of Elizabeth Blair Lee, by Virginia Jeans Laas. The correspondence also contains letters by family members such as his brother, John Fitzgerald Lee (1813-1884), and sister, Frances A. Lee (1837-1889), as well as miscellaneous Blair and Lee family members. Also included are naval personnel such as surgeon John Croxall Palmer (1811-1883), scientist John Mercer Brooke (1826-1906), Gideon Welles (1802-1878), secretary of the navy during the Civil War, and Alexander Dallas Bache (1806-1867), superintendent of the Coast Survey. Many of the letters deal with promotions, transfers, and requests for supplies.

The documents contain both personal (naval appointments, powers of attorney, wills, and financial papers) and real estate (tax receipts, deeds, leases, insurance policies, and memoranda of agreement). About a quarter of Lee's papers contain naval records, coal records, lists of officers, passengers, and seamen, descriptions of ships, and prizes, to name but a few, for ships such as the Brandywine, Young Rover, Vandalia, Newborn, Dolphin, Severn, and Worcester. There are 101 maps in the collection pertaining to Lee's duty with the U.S. Coast Survey and later during the Civil War as commander of the North Atlantic Blockading Squadron and the Mississippi Squadron. The papers of others contain mainly family correspondence.